view test-data/mut.tabular @ 3:525c661a7fdc draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587

Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_Position	End_Position	Strand	Consequence	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_File	Sequencer	t_ref_count	t_alt_count	n_ref_count	n_alt_count	HGVSc	HGVSp	HGVSp_Short	Transcript_ID	RefSeq	Protein_position	Codons	Hotspot	gc_content	ref_context
NOS1	4842	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	117669890	117669890	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21	19			ENST00000338101.4:c.3384C>T	p.Thr1128=	p.T1128=	ENST00000338101		1128	acC/acT	0	0.592	CCTGGAAGATGGTGCAGGGCG
NPAS3	64067	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	14	34263252	34263252	+	splice_donor_variant	Splice_Site	SNP	T	T	G			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	44	26			ENST00000356141.4:c.1301+2T>G		p.X434_splice	ENST00000356141				0	0.333	CCTTCTTAGGTATATTTTCTA
JAG2	3714	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	14	105615619	105615619	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	85	48			ENST00000331782.3:c.1641C>T	p.Asn547=	p.N547=	ENST00000331782	NM_002226.4	547	aaC/aaT	0	0.662	AGCGAGCGCCGTTCCGGCAGG
ENKD1	84080	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	67700039	67700039	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52	8			ENST00000243878.4:c.215G>A	p.Arg72His	p.R72H	ENST00000243878	NM_032140.1	72	cGc/cAc	0	0.662	CCCGACGCCGCGCTGGCCGCG
FKBP8	23770	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	18650228	18650228	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	50	51			ENST00000608443.1:c.504G>A	p.Thr168=	p.T168=	ENST00000608443		168	acG/acA	0	0.637	TGACCATGGCCGTCTCCCCCA
IRF2BP1	26145	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	46387378	46387378	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4	15			ENST00000302165.3:c.1655G>T	p.Cys552Phe	p.C552F	ENST00000302165	NM_015649.1	552	tGc/tTc	0	0.642	GACCAGCGGGCACTTGTCTCC
PHACTR3	116154	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	20	58381107	58381107	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	287	69			ENST00000371015.1:c.1186C>T	p.Arg396Trp	p.R396W	ENST00000371015	NM_080672.4	396	Cgg/Tgg	0	0.547	AACACTGCCACGGAAATGCAA
KRTAP13-1	140258	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	21	31768834	31768834	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17	17			ENST00000355459.2:c.430G>A	p.Val144Ile	p.V144I	ENST00000355459	NM_181599.2	144	Gtt/Att	0	0.542	GGGCTATGGCGTTGGATTCTG
PWP2	5822	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	21	45540355	45540355	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	101	81			ENST00000291576.7:c.1315G>A	p.Val439Met	p.V439M	ENST00000291576	NM_005049.2	439	Gtg/Atg	0	0.597	GGACGGGACCGTGCGAGCCTT
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62	26			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
TXK	7294	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	48114404	48114404	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	148	27			ENST00000264316.4:c.300T>C	p.Asn100=	p.N100=	ENST00000264316	NM_003328.2	100	aaT/aaC	0	0.468	TTAAGGCTAAATTACAGGGTT
NPY1R	4886	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	164247119	164247119	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39	35			ENST00000296533.2:c.588C>T	p.Tyr196=	p.Y196=	ENST00000296533	NM_000909.5	196	taC/taT	0	0.408	CAAAGCACACGTATTTGTCTT
PLEKHG4B	153478	hgsc.bcm.edu;broad.mit.edu	GRCh37	5	143249	143249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs115149634	byFrequency	TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74	22			ENST00000283426.6:c.497G>A	p.Arg166Gln	p.R166Q	ENST00000283426	NM_052909.3	166	cGg/cAg	0	0.647	GTGCCTGCCCGGCAGCCACAC
ZDHHC11	79844	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	814876	814876	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs138424733		TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	34	26			ENST00000283441.8:c.1181G>C	p.Gly394Ala	p.G394A	ENST00000283441	NM_024786.2	394	gGg/gCg	0	0.378	ACGAACTTACCCAAGTGTAGA
DNAH8	1769	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	38690599	38690599	+	upstream_gene_variant	5'Flank	SNP	C	C	T			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15	11						ENST00000359357				0	0.532	GAGAAGGATGCTGAAGATGGC
THEMIS	387357	hgsc.bcm.edu;broad.mit.edu	GRCh37	6	128135074	128135074	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	55	40			ENST00000543064.1:c.712C>T	p.Arg238Ter	p.R238*	ENST00000543064	NM_001164685.1	238	Cga/Tga	0	0.333	ATATCTTTTCGAACTAAAAAG
ZNF782	158431	hgsc.bcm.edu;broad.mit.edu	GRCh37	9	99581580	99581580	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	92	8			ENST00000481138.1:c.725C>G	p.Ser242Cys	p.S242C	ENST00000481138	NM_001001662.1	242	tCt/tGt	0	0.333	GAAATTGTAAGATTTTCCTTT
FRMPD4	9758	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	12701668	12701668	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3	28			ENST00000380682.1:c.535C>T	p.Arg179Cys	p.R179C	ENST00000380682	NM_014728.3	179	Cgc/Tgc	0	0.423	TGTCAAAGTACGCTTCTCTGA
CEP104	9731	broad.mit.edu;ucsc.edu	GRCh37	1	3768869	3768869	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21	3			ENST00000378230.3:c.103C>T	p.Arg35Trp	p.R35W	ENST00000378230	NM_014704.3	35	Cgg/Tgg	0	0.622	CTAGGTGACCGCCACCCACTG
NF1	4763	broad.mit.edu;ucsc.edu	GRCh37	17	29670155	29670155	+	splice_donor_variant	Splice_Site	SNP	T	T	A			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36	5			ENST00000358273.4:c.7189+2T>A		p.X2397_splice	ENST00000358273	NM_001042492.2			0	0.318	TTTTAAAAGGTAAAAAAGCCT
HLA-J	3137	broad.mit.edu;ucsc.edu	GRCh37	6	29977359	29977359	+	non_coding_transcript_exon_variant,non_coding_transcript_variant	RNA	SNP	G	G	A	rs3831361	by1000genomes	TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47	7			ENST00000462773.1:n.932G>A		*311*	ENST00000462773				0	0.453	ATTTGTTCATGCCTTCCCTTT
TRBV7-6	28592	broad.mit.edu;ucsc.edu	GRCh37	7	142139349	142139349	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96	26			ENST00000390374.3:c.276C>T	p.Ser92=	p.S92=	ENST00000390374		92	tcC/tcT	0	0.567	GAGTGGAGACGGATCCCTCAG
HLA-J	3137	broad.mit.edu;ucsc.edu	GRCh37	6	29977358	29977358	+	non_coding_transcript_exon_variant,non_coding_transcript_variant	RNA	SNP	T	T	C	rs146982767	by1000genomes	TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47	7			ENST00000462773.1:n.931T>C		*311*	ENST00000462773				0	0.448	GATTTGTTCATGCCTTCCCTT
NPTX1	4884	broad.mit.edu;ucsc.edu	GRCh37	17	78444660	78444660	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	51	7			ENST00000306773.4:c.1252G>A	p.Gly418Arg	p.G418R	ENST00000306773	NM_002522.3	418	Gga/Aga	0	0.662	GTGGCCCCTCCGTAGATCTCG
NT5C	30833	broad.mit.edu;ucsc.edu	GRCh37	17	73126675	73126675	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47	30			ENST00000245552.2:c.514G>T	p.Val172Phe	p.V172F	ENST00000245552	NM_014595.2	172	Gtc/Ttc	0	0.607	GGGGGCAGGACCAGGTGCCGA
SMC4	10051	broad.mit.edu;ucsc.edu	GRCh37	3	160137299	160137299	+	missense_variant	Missense_Mutation	SNP	T	T	A			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57	35			ENST00000357388.3:c.1825T>A	p.Ser609Thr	p.S609T	ENST00000357388	NM_001002800.1	609	Tct/Act	0	0.343	AGAAAAAAAATCTGGCAGGAT
FUBP1	8880	broad.mit.edu;hgsc.bcm.edu	GRCh37	1	78433848	78433851	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CAGT	CAGT	-			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11	20			ENST00000370768.2:c.248_250+1delACTG		p.X83_splice	ENST00000370768	NM_003902.3	83		0	0.319	GGAATACTTACAGTCATTTTGAGG
HGD	3081	broad.mit.edu;hgsc.bcm.edu	GRCh37	3	120357338	120357338	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	92	23			ENST00000283871.5:c.970delG	p.Val324LeufsTer16	p.V324Lfs*16	ENST00000283871	NM_000187.3	324	Gtt/tt	0	0.483	TTATCAGCAACCCCCCATCGA
WDFY3	23001	broad.mit.edu;hgsc.bcm.edu	GRCh37	4	85731329	85731331	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	51	28			ENST00000295888.4:c.2054_2056delTTC	p.Leu685del	p.L685del	ENST00000295888	NM_014991.4	685	cTTCac/cac	0	0.448	AACACAGTGTGAAGAAGTTCAAA
MAN2A1	4124	broad.mit.edu;hgsc.bcm.edu	GRCh37	5	109049430	109049433	+	frameshift_variant	Frame_Shift_Del	DEL	CTGT	CTGT	-			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	133	38			ENST00000261483.4:c.349_352delCTGT	p.Phe118LeufsTer19	p.F118Lfs*19	ENST00000261483	NM_002372.2	115	gaCTGT/ga	0	0.407	ACACTGCAGACTGTCTGTTTGCTT
HDAC2	3066	broad.mit.edu;hgsc.bcm.edu	GRCh37	6	114277842	114277844	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	16	15			ENST00000519065.1:c.297_299delAGA	p.Glu99del	p.E99del	ENST00000519065		99	gaAGAt/gat	0	0.35	CACTGGACAATCTTCTCCAACAT
NOTCH1	4851	broad.mit.edu;hgsc.bcm.edu	GRCh37	9	139391997	139391998	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14	17			ENST00000277541.6:c.6193_6194delCT	p.Leu2065ValfsTer202	p.L2065Vfs*202	ENST00000277541	NM_017617.3	2065	CTg/g	0	0.683	GGCCAGAAACAGGGGTGTCTCC
NOTCH1	4851	broad.mit.edu;hgsc.bcm.edu	GRCh37	9	139395163	139395166	+	frameshift_variant	Frame_Shift_Del	DEL	GTCT	GTCT	-			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	136	41			ENST00000277541.6:c.5772_5775delAGAC	p.Asp1925AlafsTer55	p.D1925Afs*55	ENST00000277541	NM_017617.3	1924	acAGAC/ac	0	0.686	CGCCCGTGCGGTCTGTCTGGTTGT
PHLPP2	23035	broad.mit.edu;hgsc.bcm.edu	GRCh37	16	71692597	71692599	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	rs145938775		TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	133	25			ENST00000568954.1:c.2105_2107delACA	p.Asn702del	p.N702del	ENST00000568954		702	aACAtc/atc	0	0.458	AAAATGCTGATGTTGTTGGAGTG
PLIN4	729359	broad.mit.edu;hgsc.bcm.edu	GRCh37	19	4510914	4510916	+	inframe_deletion	In_Frame_Del	DEL	TGG	TGG	-			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28	22			ENST00000301286.3:c.3014_3016delCCA	p.Thr1005del	p.T1005del	ENST00000301286	NM_001080400.1	1005	aCCAag/aag	0	0.626	AGCACTGTCTTGGTGGTGTCCAG
NF1	4763	broad.mit.edu	GRCh37	17	29546036	29546037	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	13	7			ENST00000358273.4:c.1541_1542delAG	p.Gln514ArgfsTer43	p.Q514Rfs*43	ENST00000358273	NM_001042492.2	514	cAG/c	0	0.426	CCAAGAAAACAGGGGCCCGAAA
PIK3R1	5295	broad.mit.edu	GRCh37	5	67591105	67591107	+	inframe_deletion	In_Frame_Del	DEL	TAA	TAA	-			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	108	16			ENST00000274335.5:c.1698_1700delTAA	p.Lys567del	p.K567del	ENST00000274335		566	atTAAa/ata	0	0.369	TGAACAGCATTAAACCAGACCTT
NF1	4763	broad.mit.edu	GRCh37	17	29652976	29652979	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	168	11			ENST00000358273.4:c.4977_4980delCTCT	p.Lys1661GlyfsTer36	p.K1661Gfs*36	ENST00000358273	NM_001042492.2	1658	ttTCTC/tt	0	0.422	AAACAGACTTTCTCTCTAAGTGGT
NF1	4763	broad.mit.edu	GRCh37	17	29553697	29553697	+	stop_gained	Nonsense_Mutation	SNP	C	C	A			TCGA-DU-6394-01	TCGA-DU-6394-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	162	7			ENST00000358273.4:c.2246C>A	p.Ser749Ter	p.S749*	ENST00000358273	NM_001042492.2	749	tCa/tAa	0	0.403	AATATGATGTCAACAGGTAAA
CUBN	8029	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	16992025	16992025	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-FG-8187-01	TCGA-FG-8187-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40	16			ENST00000377833.4:c.5055C>T	p.Gly1685=	p.G1685=	ENST00000377833	NM_001081.3	1685	ggC/ggT	0	0.448	CTTCGTGGCCGCCATCCAAAA
OR8K1	390157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	56114203	56114203	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-FG-8187-01	TCGA-FG-8187-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	51	27			ENST00000279783.2:c.689C>T	p.Ala230Val	p.A230V	ENST00000279783	NM_001002907.1	230	gCc/gTc	0	0.383	ATTCTAGTGGCCATTCTCAGA
PBX4	80714	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	19672911	19672911	+	stop_gained	Nonsense_Mutation	SNP	G	G	A			TCGA-FG-8187-01	TCGA-FG-8187-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	27	4			ENST00000251203.9:c.1048C>T	p.Gln350Ter	p.Q350*	ENST00000251203	NM_025245.2	350	Cag/Tag	0	0.597	GTGGCCCCCTGCCAGCTACCC
FAM89A	375061	hgsc.bcm.edu;broad.mit.edu	GRCh37	1	231155648	231155648	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-FG-8187-01	TCGA-FG-8187-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58	3			ENST00000366654.4:c.516C>T	p.Ser172=	p.S172=	ENST00000366654	NM_198552.2	172	tcC/tcT	0	0.567	TGGAGAGGGAGGAGACAGGCA
RIPK4	54101	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	21	43166845	43166845	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-FG-8187-01	TCGA-FG-8187-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96	69			ENST00000332512.3:c.760G>A	p.Ala254Thr	p.A254T	ENST00000332512	NM_020639.2	254	Gcc/Acc	0	0.672	TGGCTGCAGGCGCGCGGCCGG
MYO7B	4648	hgsc.bcm.edu;ucsc.edu	GRCh37	2	128367552	128367552	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-FG-8187-01	TCGA-FG-8187-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33	4			ENST00000428314.1:c.3153G>A	p.Glu1051=	p.E1051=	ENST00000428314	NM_001080527.1	1051	gaG/gaA	0	0.642	TGGGCAGGGAGCACGGTGCCC
HOXD3	3232	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	177034190	177034190	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-FG-8187-01	TCGA-FG-8187-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	44	17			ENST00000468418.3:c.348A>G	p.Pro116=	p.P116=	ENST00000468418		116	ccA/ccG	0	0.642	AGCAGCAGccaccacaacccc
ZDBF2	57683	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	207175936	207175936	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-FG-8187-01	TCGA-FG-8187-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17	10			ENST00000374423.3:c.6684G>A	p.Ser2228=	p.S2228=	ENST00000374423	NM_020923.1	2228	tcG/tcA	0	0.363	AGTATATTTCGAAATACTCTG
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-FG-8187-01	TCGA-FG-8187-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	121	44			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
PIK3CA	5290	hgsc.bcm.edu;broad.mit.edu	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279		TCGA-FG-8187-01	TCGA-FG-8187-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	109	8			ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	0	0.378	AATGATGCACATCATGGTGGC
CERCAM	51148	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	131186792	131186792	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-FG-8187-01	TCGA-FG-8187-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69	39			ENST00000372838.4:c.665G>A	p.Arg222Gln	p.R222Q	ENST00000372838	NM_016174.4	222	cGg/cAg	0	0.617	GCATCCCTGCGGGCTGAAGGG
KCNQ4	9132	broad.mit.edu;ucsc.edu	GRCh37	1	41283890	41283890	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-FG-8187-01	TCGA-FG-8187-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58	23			ENST00000347132.5:c.460G>A	p.Ala154Thr	p.A154T	ENST00000347132	NM_004700.3	154	Gcc/Acc	0	0.612	GGTCTGGTCCGCCGGATGCTG
SLC9A7P1	121456	broad.mit.edu;ucsc.edu	GRCh37	12	98850610	98850610	+	non_coding_transcript_exon_variant	RNA	SNP	C	C	A			TCGA-FG-8187-01	TCGA-FG-8187-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15	5			ENST00000554295.1:n.314G>T		*105*	ENST00000554295				0	0.602	AAAGTGCACCCGGCAGTACTT
TEKT1	83659	broad.mit.edu;ucsc.edu	GRCh37	17	6703471	6703471	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-FG-8187-01	TCGA-FG-8187-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	135	12			ENST00000338694.2:c.1132G>A	p.Val378Ile	p.V378I	ENST00000338694	NM_053285.1	378	Gtc/Atc	0	0.527	TTCTCTTTGACCTGGATCTCC
GPR114	221188	hgsc.bcm.edu;ucsc.edu	GRCh37	16	57601804	57601804	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs146006750		TCGA-CS-4938-01	TCGA-CS-4938-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	44	5			ENST00000340339.4:c.858C>A	p.Asn286Lys	p.N286K	ENST00000340339	NM_153837.1	286	aaC/aaA	0	0.612	TCCACATGAACCTGCATGCCT
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651		TCGA-CS-4938-01	TCGA-CS-4938-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21	86			ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	0	0.577	ATGGGCCTCCGGTTCATGCCG
C3	718	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	6686853	6686853	+	stop_gained	Nonsense_Mutation	SNP	G	G	A			TCGA-CS-4938-01	TCGA-CS-4938-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	127	21			ENST00000245907.6:c.3550C>T	p.Gln1184Ter	p.Q1184*	ENST00000245907	NM_000064.2	1184	Cag/Tag	0	0.512	TAGGATCTCTGTAGGTTCATG
KLK10	5655	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	51518742	51518742	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-CS-4938-01	TCGA-CS-4938-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258	124			ENST00000309958.3:c.609C>T	p.Val203=	p.V203=	ENST00000309958	NM_002776.4	203	gtC/gtT	0	0.552	CAGGGTAGAAGACCTCACACT
ANXA9	8416	hgsc.bcm.edu;broad.mit.edu	GRCh37	1	150955565	150955565	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A			TCGA-CS-4938-01	TCGA-CS-4938-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	77	6			ENST00000368947.4:c.-16-1G>A		p.X6_splice	ENST00000368947	NM_003568.2			0	0.622	TCCTTCCCCAGGGCAACCAGT
TPO	7173	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	1499888	1499888	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-CS-4938-01	TCGA-CS-4938-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	51	10			ENST00000345913.4:c.2134G>A	p.Gly712Ser	p.G712S	ENST00000345913	NM_000547.5	712	Ggc/Agc	0	0.562	CTTCCAAGTCGGCAAATTCCC
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-CS-4938-01	TCGA-CS-4938-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52	29			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
LEPREL1	55214	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	189705423	189705423	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-CS-4938-01	TCGA-CS-4938-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	106	30			ENST00000319332.5:c.991G>T	p.Ala331Ser	p.A331S	ENST00000319332	NM_018192.3	331	Gcc/Tcc	0	0.468	AGAAGATAGGCTTTGGCACAC
FGF5	2250	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	81207632	81207632	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-CS-4938-01	TCGA-CS-4938-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	101	49			ENST00000312465.7:c.613C>G	p.Arg205Gly	p.R205G	ENST00000312465	NM_004464.3	205	Cgg/Ggg	0	0.463	GTGCAGCCCCCGGGTTAAACC
ENPEP	2028	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	111441429	111441429	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-CS-4938-01	TCGA-CS-4938-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	44	34			ENST00000265162.5:c.1634C>G	p.Pro545Arg	p.P545R	ENST00000265162	NM_001977.3	545	cCt/cGt	0	0.428	ATGGGTTATCCTGTGCTTAAC
ADAD1	132612	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	123336616	123336616	+	synonymous_variant	Silent	SNP	A	A	T			TCGA-CS-4938-01	TCGA-CS-4938-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	116	70			ENST00000296513.2:c.1332A>T	p.Pro444=	p.P444=	ENST00000296513	NM_139243.3	444	ccA/ccT	0	0.378	CAAAACTTCCAATGTTTTACT
TKTL2	84076	hgsc.bcm.edu;broad.mit.edu	GRCh37	4	164393959	164393959	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-CS-4938-01	TCGA-CS-4938-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	228	14			ENST00000280605.3:c.928C>G	p.Pro310Ala	p.P310A	ENST00000280605	NM_032136.4	310	Cca/Gca	0	0.408	taagcaggtggggaggtcatt
ADAM22	53616	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	87757957	87757957	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-CS-4938-01	TCGA-CS-4938-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	146	16			ENST00000265727.7:c.719A>G	p.Tyr240Cys	p.Y240C	ENST00000265727		240	tAc/tGc	0	0.403	GAAACCAAATACATTGAACTG
KDM7A	80853	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	139824520	139824520	+	missense_variant	Missense_Mutation	SNP	T	T	G			TCGA-CS-4938-01	TCGA-CS-4938-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33	18			ENST00000397560.2:c.952A>C	p.Ser318Arg	p.S318R	ENST00000397560	NM_030647.1	318	Agt/Cgt	0	0.358	ACAGATGAACTCCAAGATTCA
ACTRT1	139741	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	127186136	127186136	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-CS-4938-01	TCGA-CS-4938-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68	40			ENST00000371124.3:c.50G>T	p.Gly17Val	p.G17V	ENST00000371124	NM_138289.3	17	gGt/gTt	0	0.433	GAGTCCTGAACCATTGTCAAA
ZNF185	7739	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	152083048	152083048	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-CS-4938-01	TCGA-CS-4938-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7	8			ENST00000535861.1:c.15T>C	p.Ala5=	p.A5=	ENST00000535861	NM_001178106.1	5	gcT/gcC	0	0.547	GTATCTCAGCTCTTGGAGGCC
TTLL7	79739	broad.mit.edu;ucsc.edu	GRCh37	1	84356051	84356051	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-CS-4938-01	TCGA-CS-4938-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33	29			ENST00000260505.8:c.2322A>G	p.Leu774=	p.L774=	ENST00000260505	NM_024686.4	774	ttA/ttG	0	0.378	GACTCCAGAGTAAGCGATTAA
ATRX	546	broad.mit.edu;hgsc.bcm.edu	GRCh37	X	76939674	76939674	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-			TCGA-CS-4938-01	TCGA-CS-4938-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	143	100			ENST00000373344.5:c.1074delA	p.Lys358AsnfsTer2	p.K358Nfs*2	ENST00000373344	NM_000489.3	358	aaA/aa	0	0.368	TCTCAATCAGTTTTTTTGCCT
RPP30	10556	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	92631801	92631801	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	94	69			ENST00000413330.1:c.58G>A	p.Gly20Arg	p.G20R	ENST00000413330	NM_001104546.1	20	Gga/Aga	0	0.637	GGCTCTGCGCGGACTTGTGGA
SPA17	53340	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	124564278	124564278	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98	17			ENST00000532692.1:c.392G>A	p.Arg131Lys	p.R131K	ENST00000532692		131	aGa/aAa	0	0.408	CACATAGCCAGAGAGGAGGCA
M6PR	4074	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	9094479	9094479	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	449	57			ENST00000000412.3:c.769G>A	p.Gly257Ser	p.G257S	ENST00000000412	NM_002355.3	257	Ggt/Agt	0	0.468	TCCCCCACACCACGATATGCT
GPRC5D	55507	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	13102595	13102595	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	86	15			ENST00000228887.1:c.724G>A	p.Val242Ile	p.V242I	ENST00000228887	NM_018654.1	242	Gtc/Atc	0	0.567	GCAATGCAGACGACCGGGTCG
DNAH10	196385	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	124332564	124332564	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	38	57			ENST00000409039.3:c.5517C>T	p.Thr1839=	p.T1839=	ENST00000409039	NM_207437.3	1839	acC/acT	0	0.552	CCGGCAAAACCGAGACCACCA
COL4A2	1284	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	13	111147702	111147702	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	111	12			ENST00000360467.5:c.3648C>T	p.His1216=	p.H1216=	ENST00000360467	NM_001846.2	1216	caC/caT	0	0.557	CTGACATCCACGGAGACCCAG
NPAP1	23742	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	24921762	24921762	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61	12			ENST00000329468.2:c.748C>T	p.Arg250Trp	p.R250W	ENST00000329468	NM_018958.2	250	Cgg/Tgg	0	0.622	CGGATGTGCCCGGCATCTTGG
GPR139	124274	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	20043246	20043246	+	synonymous_variant	Silent	SNP	C	C	G			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	132	21			ENST00000570682.1:c.873G>C	p.Arg291=	p.R291=	ENST00000570682	NM_001002911.2	291	cgG/cgC	0	0.502	TGGTGCGGAACCGCTTGCTGA
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	G	rs68140816		TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	16	56			ENST00000269305.4:c.375+1G>C		p.X125_splice	ENST00000269305	NM_001126112.2			0	0.532	GGGCAACTGACCGTGCAAGTC
HELZ	9931	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	65105453	65105453	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	48	29			ENST00000358691.5:c.4268A>G	p.Tyr1423Cys	p.Y1423C	ENST00000358691	NM_014877.3	1423	tAt/tGt	0	0.527	TCCCGCCTGATATGCAGGAGA
TTYH2	94015	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	72246149	72246149	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58	38			ENST00000269346.4:c.1005C>T	p.Pro335=	p.P335=	ENST00000269346	NM_032646.5	335	ccC/ccT	0	0.652	TTGCCGTGCCCCTCTTCTCCA
ACER1	125981	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	6307219	6307219	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	49	12			ENST00000301452.4:c.571C>T	p.Arg191Cys	p.R191C	ENST00000301452	NM_133492.2	191	Cgt/Tgt	0	0.542	CAAAGCAGACGGTCACTGATC
GPR32	2854	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	51273893	51273893	+	missense_variant	Missense_Mutation	SNP	T	T	A			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17	7			ENST00000270590.4:c.36T>A	p.Ser12Arg	p.S12R	ENST00000270590	NM_001506.2	12	agT/agA	0	0.498	GAGGCTGCAGTGACAGGCAAC
BSDC1	55108	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	32842101	32842101	+	synonymous_variant	Silent	SNP	G	G	T			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	63	42			ENST00000446293.2:c.969C>A	p.Ser323=	p.S323=	ENST00000446293		323	tcC/tcA	0	0.597	GCAGCTTTTGGGACAGGTCCT
PCIF1	63935	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	20	44567656	44567656	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90	14			ENST00000372409.3:c.18C>T	p.His6=	p.H6=	ENST00000372409	NM_022104.3	6	caC/caT	0	0.602	ATGAGAATCACGGCAGCCCCC
APOBEC3H	164668	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	22	39497965	39497965	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9	29			ENST00000401756.1:c.461C>T	p.Pro154Leu	p.P154L	ENST00000401756	NM_001166003.1	154	cCg/cTg	0	0.537	CACGAGAAACCGCTTTCCTTC
TTN	7273	hgsc.bcm.edu;ucsc.edu	GRCh37	2	179613099	179613099	+	intron_variant	Intron	SNP	A	A	C			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	124	23			ENST00000589042.1:c.11311+4752T>G		*3771*	ENST00000589042	NM_001267550.1			0	0.333	GACTGGAAGAAATTTCTTGAC
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42	29			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
CNTN3	5067	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	74419100	74419100	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68	12			ENST00000263665.6:c.701C>G	p.Pro234Arg	p.P234R	ENST00000263665	NM_020872.1	234	cCa/cGa	0	0.333	AAGAGTTTCTGGAAACTGAAC
STX19	415117	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	93733522	93733522	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	66	11			ENST00000315099.2:c.592T>C	p.Leu198=	p.L198=	ENST00000315099	NM_001001850.2	198	Tta/Cta	0	0.328	TCTGTAAGTAAGCTTTCATTA
PLCH1	23007	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	155198970	155198970	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68	10			ENST00000340059.7:c.4869C>T	p.Thr1623=	p.T1623=	ENST00000340059	NM_001130960.1	1623	acC/acT	0	0.577	TCACTGCAGGGGTGGGTGCTG
ZBBX	79740	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	166960403	166960403	+	synonymous_variant	Silent	SNP	G	G	T			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	20	9			ENST00000455345.2:c.2283C>A	p.Thr761=	p.T761=	ENST00000455345		761	acC/acA	0	0.368	ACTCTTCTGAGGTTAAGCTGT
SKP2	6502	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	36152899	36152899	+	missense_variant	Missense_Mutation	SNP	T	T	A			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	50	17			ENST00000274255.6:c.35T>A	p.Leu12Gln	p.L12Q	ENST00000274255	NM_005983.3	12	cTg/cAg	0	0.517	ATTCCAGACCTGAGTAGCAAC
GABRA6	2559	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	161118969	161118969	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79	10			ENST00000274545.5:c.849G>A	p.Met283Ile	p.M283I	ENST00000274545		283	atG/atA	0	0.403	TTTTAACTATGACCACTTTGA
DLX5	1749	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	96651603	96651603	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	77	47			ENST00000222598.4:c.434C>G	p.Ser145Cys	p.S145C	ENST00000222598	NM_005221.5	145	tCc/tGc	0	0.498	CTGAAAGCTGGAATAAATAGT
PAX4	5078	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	127255046	127255046	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71	46			ENST00000341640.2:c.224C>G	p.Pro75Arg	p.P75R	ENST00000341640	NM_006193.2	75	cCt/cGt	0	0.582	AGCCACCACAGGGGGTGTAGC
KEL	3792	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	142655011	142655011	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42	16			ENST00000355265.2:c.575G>A	p.Arg192Gln	p.R192Q	ENST00000355265	NM_000420.2	192	cGa/cAa	0	0.522	TCTCAGCGTTCGGTTAAAGTT
BICD2	23299	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	95481306	95481306	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67	22			ENST00000356884.6:c.1621G>A	p.Val541Met	p.V541M	ENST00000356884	NM_001003800.1	541	Gtg/Atg	0	0.657	CACATGCACACGTGGTGGTAG
DBH	1621	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	136501814	136501814	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26	7			ENST00000393056.2:c.321G>A	p.Gly107=	p.G107=	ENST00000393056	NM_000787.3	107	ggG/ggA	0	0.617	GGACCGATGGGGACACTGCCT
COL4A5	1287	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	107938508	107938508	+	synonymous_variant	Silent	SNP	A	A	T			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58	19			ENST00000328300.6:c.4833A>T	p.Ala1611=	p.A1611=	ENST00000328300	NM_033380.2	1611	gcA/gcT	0	0.488	ATACAAGTGCAGGGGCAGAAG
ZNF629	23361	broad.mit.edu;ucsc.edu	GRCh37	16	30795077	30795077	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	38	4			ENST00000262525.4:c.572C>T	p.Ser191Leu	p.S191L	ENST00000262525	NM_001080417.1	191	tCg/tTg	0	0.657	CACCAGGTGCGAGCTCTGCGT
OLFM3	118427	broad.mit.edu;ucsc.edu	GRCh37	1	102290602	102290602	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	44	7			ENST00000370103.4:c.572G>A	p.Arg191His	p.R191H	ENST00000370103	NM_058170.2	191	cGt/cAt	0	0.373	CATGCAGTCACGAAGTCTTGT
MUC17	140453	broad.mit.edu;ucsc.edu	GRCh37	7	100679309	100679309	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257	46			ENST00000306151.4:c.4612C>G	p.Pro1538Ala	p.P1538A	ENST00000306151	NM_001040105.1	1538	Cct/Gct	0	0.473	TTCAACAACTCCTGCTGTCAC
COL14A1	7373	broad.mit.edu;ucsc.edu	GRCh37	8	121290392	121290392	+	stop_gained	Nonsense_Mutation	SNP	A	A	T			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	63	52			ENST00000297848.3:c.3256A>T	p.Lys1086Ter	p.K1086*	ENST00000297848	NM_021110.2	1086	Aaa/Taa	0	0.378	AACAGAATTTAAACTAAATGC
CXXC4	80319	broad.mit.edu;ucsc.edu	GRCh37	4	105412082	105412082	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61	13			ENST00000394767.2:c.878G>A	p.Gly293Glu	p.G293E	ENST00000394767	NM_025212.2	293	gGg/gAg	0	0.602	GCCAGCTCCCCCTGAGGAGGA
CCDC33	80125	broad.mit.edu;ucsc.edu	GRCh37	15	74554908	74554908	+	stop_gained	Nonsense_Mutation	SNP	C	C	T			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	13	4			ENST00000398814.3:c.313C>T	p.Gln105Ter	p.Q105*	ENST00000398814	NM_025055.4	105	Caa/Taa	0	0.597	GGATGCAGGGCAAGAAGGTAA
ROS1	6098	broad.mit.edu;hgsc.bcm.edu	GRCh37	6	117746774	117746774	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90	60			ENST00000368508.3:c.46delA	p.Thr16LeufsTer15	p.T16Lfs*15	ENST00000368508	NM_002944.2	16	Act/ct	0	0.378	CAGCCAAGAGTTGCAAAATTG
METAP2	10988	broad.mit.edu;hgsc.bcm.edu	GRCh37	12	95868076	95868078	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45	11			ENST00000323666.5:c.131_133delAGA	p.Lys44del	p.K44del	ENST00000323666	NM_006838.3	41	AAG/-	0	0.557	AAAAAGACGAAAGAAGAAGAAGA
ATRX	546	broad.mit.edu	GRCh37	X	76814313	76814313	+	stop_gained	Nonsense_Mutation	SNP	G	G	A			TCGA-DU-7007-01	TCGA-DU-7007-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6	15			ENST00000373344.5:c.6331C>T	p.Arg2111Ter	p.R2111*	ENST00000373344	NM_000489.3	2111	Cga/Tga	0	0.274	ATAAATAATCGTCCTCTGAAA
CD163	9332	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	7635248	7635248	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7481-01	TCGA-HT-7481-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	124	55			ENST00000359156.4:c.3238C>T	p.Arg1080Trp	p.R1080W	ENST00000359156	NM_004244.5	1080	Cgg/Tgg	0	0.428	CCTGCAAGCCGCTGTCTCTGT
KERA	11081	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	91449544	91449544	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7481-01	TCGA-HT-7481-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	160	49			ENST00000266719.3:c.515A>G	p.Asp172Gly	p.D172G	ENST00000266719	NM_007035.3	172	gAc/gGc	0	0.413	GTTCTGTAGGTCAAGAAGGGT
FSCB	84075	hgsc.bcm.edu;broad.mit.edu	GRCh37	14	44975038	44975038	+	synonymous_variant	Silent	SNP	G	G	T			TCGA-HT-7481-01	TCGA-HT-7481-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	144	12			ENST00000340446.4:c.1153C>A	p.Arg385=	p.R385=	ENST00000340446	NM_032135.3	385	Cgg/Agg	0	0.532	GAGGGAGACCGAATTTCACCA
NETO1	81832	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	18	70417415	70417415	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7481-01	TCGA-HT-7481-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	49	13			ENST00000327305.6:c.1423A>G	p.Ile475Val	p.I475V	ENST00000327305	NM_138966.3	475	Atc/Gtc	0	0.507	ATGACAAGGATATTTCTTCTG
NLRP2	55655	hgsc.bcm.edu;broad.mit.edu	GRCh37	19	55494669	55494669	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7481-01	TCGA-HT-7481-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	51	4			ENST00000543010.1:c.1603G>A	p.Val535Ile	p.V535I	ENST00000543010	NM_001174081.1	535	Gta/Ata	0	0.557	CATTGGGGACGTACAGAAGCT
FUBP1	8880	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	78420962	78420962	+	stop_gained	Nonsense_Mutation	SNP	C	C	T			TCGA-HT-7481-01	TCGA-HT-7481-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24	11			ENST00000370768.2:c.1758G>A	p.Trp586Ter	p.W586*	ENST00000370768	NM_003902.3	586	tgG/tgA	0	0.318	AGTACTCTTCCCAAGCCTTGG
HRNR	388697	hgsc.bcm.edu;broad.mit.edu	GRCh37	1	152191242	152191242	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7481-01	TCGA-HT-7481-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	319	96			ENST00000368801.2:c.2863T>C	p.Ser955Pro	p.S955P	ENST00000368801	NM_001009931.2	955	Tcc/Ccc	0	0.542	TCGTAGCTGGAGGAGTGACCT
FLRT3	23767	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	20	14306271	14306271	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7481-01	TCGA-HT-7481-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	141	18			ENST00000378053.3:c.1882A>G	p.Ser628Gly	p.S628G	ENST00000378053	NM_013281.3	628	Agt/Ggt	0	0.413	CTGCTTTCACTGTGATTGTTT
TSHZ2	128553	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	20	51873020	51873020	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7481-01	TCGA-HT-7481-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	59	19			ENST00000371497.5:c.3023C>T	p.Ala1008Val	p.A1008V	ENST00000371497	NM_173485.5	1008	gCg/gTg	0	0.468	AGCAAACATGCGGTAAAACTC
DNMT3A	1788	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	25470985	25470985	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-HT-7481-01	TCGA-HT-7481-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	55	24			ENST00000264709.3:c.776C>G	p.Ala259Gly	p.A259G	ENST00000264709	NM_175629.2	259	gCt/gGt	0	0.647	AGGCGTGGTAGCCACAGTGGG
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HT-7481-01	TCGA-HT-7481-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	77	16			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
PIK3CA	5290	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7481-01	TCGA-HT-7481-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82	14			ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	0	0.338	TTTATTAAAGGTTTTGCTATC
PIK3CA	5290	hgsc.bcm.edu;broad.mit.edu	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7481-01	TCGA-HT-7481-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	101	7			ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	0	0.368	CATGAAACAAATGAATGATGC
LMLN	89782	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	197751579	197751579	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-HT-7481-01	TCGA-HT-7481-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96	12			ENST00000420910.2:c.1687C>G	p.Leu563Val	p.L563V	ENST00000420910	NM_001136049.2	563	Cta/Gta	0	0.393	TTCCGTTTGTCTAATTCAGAA
CPEB2	132864	hgsc.bcm.edu;broad.mit.edu	GRCh37	4	15060817	15060817	+	missense_variant	Missense_Mutation	SNP	A	A	T			TCGA-HT-7481-01	TCGA-HT-7481-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	63	5			ENST00000538197.1:c.2587A>T	p.Ile863Leu	p.I863L	ENST00000538197	NM_001177382.1	863	Ata/Tta	0	0.348	ATAGGTTCAAATACGTCCTTG
UGT2B28	54490	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	70155435	70155435	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7481-01	TCGA-HT-7481-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40	31			ENST00000335568.5:c.1055G>A	p.Arg352Gln	p.R352Q	ENST00000335568	NM_053039.1	352	cGg/cAg	0	0.363	CTCAATACTCGGCTGTATAAG
GK2	2712	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	80328636	80328636	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7481-01	TCGA-HT-7481-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	100	37			ENST00000358842.3:c.719A>G	p.Tyr240Cys	p.Y240C	ENST00000358842	NM_033214.2	240	tAt/tGt	0	0.423	AATTAGGCCATAGATCTCAGA
NUP155	9631	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	37309323	37309323	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7481-01	TCGA-HT-7481-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24	9			ENST00000231498.3:c.2675A>G	p.Glu892Gly	p.E892G	ENST00000231498	NM_153485.2	892	gAa/gGa	0	0.343	TCTTTCTTTTTCAGTCTTATT
KIF6	221458	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	39513390	39513390	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7481-01	TCGA-HT-7481-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	77	32			ENST00000287152.7:c.1256G>A	p.Arg419His	p.R419H	ENST00000287152	NM_145027.4	419	cGt/cAt	0	0.358	ATGAACTTTACGCATATCCGC
DLK2	65989	hgsc.bcm.edu;broad.mit.edu	GRCh37	6	43418774	43418774	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7481-01	TCGA-HT-7481-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71	5			ENST00000357338.3:c.655C>T	p.Arg219Cys	p.R219C	ENST00000357338	NM_206539.1	219	Cgc/Tgc	0	0.622	TGGCATGGGCGGCTGGCACAG
FRK	2444	hgsc.bcm.edu;broad.mit.edu	GRCh37	6	116265543	116265543	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7481-01	TCGA-HT-7481-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67	4			ENST00000606080.1:c.1004C>T	p.Ala335Val	p.A335V	ENST00000606080	NM_002031.2	335	gCg/gTg	0	0.418	AACCTGTGCCGCCATGTCTAC
MAP3K4	4216	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	161470895	161470895	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-HT-7481-01	TCGA-HT-7481-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	100	13			ENST00000392142.4:c.1591G>C	p.Asp531His	p.D531H	ENST00000392142	NM_005922.2	531	Gac/Cac	0	0.423	ACCATTTGTAGACAAAGCACT
RAB11FIP1	80223	hgsc.bcm.edu;broad.mit.edu	GRCh37	8	37734856	37734856	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7481-01	TCGA-HT-7481-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	173	13			ENST00000330843.4:c.585C>T	p.Ser195=	p.S195=	ENST00000330843	NM_001002814.2	195	agC/agT	0	0.448	AAGGTGTCGTGCTAGGGATGA
WISP2	8839	broad.mit.edu;ucsc.edu	GRCh37	20	43348625	43348625	+	missense_variant	Missense_Mutation	SNP	T	T	G			TCGA-HT-7481-01	TCGA-HT-7481-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	16	5			ENST00000372868.2:c.148T>G	p.Cys50Gly	p.C50G	ENST00000372868		50	Tgt/Ggt	0	0.697	GCTGGATGGCTGTGGCTGCTG
HIST1H2BF	8343	broad.mit.edu;hgsc.bcm.edu	GRCh37	6	26199854	26199856	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs150784470		TCGA-HT-7481-01	TCGA-HT-7481-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	131	61			ENST00000359985.1:c.73_75delAAG	p.Lys25del	p.K25del	ENST00000359985	NM_003522.3	23	cAGAag/cag	0	0.522	ACCAAGGCGCAGAAGAAGGATGG
BACH2	60468	broad.mit.edu;hgsc.bcm.edu	GRCh37	6	90660233	90660235	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-			TCGA-HT-7481-01	TCGA-HT-7481-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	63	19			ENST00000257749.4:c.1590_1592delGGA	p.Glu530del	p.E530del	ENST00000257749	NM_021813.2	530	gaGGAc/gac	0	0.616	CCCGCTCCCGTCCTCCGCGTAGG
NOTCH1	4851	broad.mit.edu	GRCh37	9	139413067	139413069	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-			TCGA-HT-7481-01	TCGA-HT-7481-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29	7			ENST00000277541.6:c.1073_1075delACT	p.Tyr358del	p.Y358del	ENST00000277541	NM_017617.3	358	tACTgc/tgc	0	0.655	GGACACTCGCAGTAGAAGGAGGC
PIK3CA	5290	broad.mit.edu	GRCh37	3	178928078	178928080	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-			TCGA-HT-7481-01	TCGA-HT-7481-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	102	8			ENST00000263967.3:c.1359_1361delAGA	p.Glu453del	p.E453del	ENST00000263967	NM_006218.2	452	ttAGAa/tta	0	0.35	CTCATGGATTAGAAGATTTGCTG
PIK3R1	5295	broad.mit.edu	GRCh37	5	67589147	67589149	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-			TCGA-HT-7481-01	TCGA-HT-7481-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69	11			ENST00000274335.5:c.1135_1137delAAA	p.Lys379del	p.K379del	ENST00000274335		379	AAA/-	0	0.31	GGGAAATAACAAATTAATCAAAA
TRIM51	84767	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	55655604	55655604	+	stop_gained	Nonsense_Mutation	SNP	C	C	T			TCGA-DU-5872-01	TCGA-DU-5872-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42	22			ENST00000449290.2:c.604C>T	p.Arg202Ter	p.R202*	ENST00000449290	NM_032681.3	202	Cga/Tga	0	0.433	GGAAAGGCTGCGAAAGGAGGG
PRICKLE1	144165	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	42858963	42858963	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-DU-5872-01	TCGA-DU-5872-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	27	19			ENST00000455697.1:c.873T>C	p.Cys291=	p.C291=	ENST00000455697	NM_001144883.1	291	tgT/tgC	0	0.522	GAAGGAAGGGACATCCCAACA
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-DU-5872-01	TCGA-DU-5872-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15	45			ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	0	0.642	GCAGCGCTCATGGTGGGGGCA
PSMD12	5718	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	65341917	65341917	+	synonymous_variant	Silent	SNP	T	T	A			TCGA-DU-5872-01	TCGA-DU-5872-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	38	27			ENST00000356126.3:c.852A>T	p.Ser284=	p.S284=	ENST00000356126	NM_002816.3	284	tcA/tcT	0	0.358	GAACCAAATCTGACTGTTCAT
LAMA3	3909	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	18	21425086	21425086	+	splice_region_variant,synonymous_variant	Splice_Region	SNP	T	T	G			TCGA-DU-5872-01	TCGA-DU-5872-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	20	16			ENST00000313654.9:c.3717T>G	p.Leu1239=	p.L1239=	ENST00000313654	NM_198129.1	1239	ctT/ctG	0	0.493	GCTTTTACCTTGAGTGAGTAT
RERE	473	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	8421423	8421423	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-DU-5872-01	TCGA-DU-5872-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39	23			ENST00000337907.3:c.2144T>C	p.Ile715Thr	p.I715T	ENST00000337907	NM_012102.3	715	aTc/aCc	0	0.627	GGGGCTGGGGATGCTCGGGGA
TAS1R2	80834	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	19166820	19166820	+	stop_gained	Nonsense_Mutation	SNP	G	G	T			TCGA-DU-5872-01	TCGA-DU-5872-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45	26			ENST00000375371.3:c.1793C>A	p.Ser598Ter	p.S598*	ENST00000375371	NM_152232.2	598	tCg/tAg	0	0.647	GCCCCCAGCCGAGCGAACTAT
COL11A1	1301	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	103380351	103380351	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-5872-01	TCGA-DU-5872-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	22	12			ENST00000370096.3:c.3833G>A	p.Arg1278Lys	p.R1278K	ENST00000370096	NM_001854.3	1278	aGa/aAa	0	0.453	TTTCTCTCCTCTTTCTCCTTT
PIAS3	10401	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	145585437	145585437	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-DU-5872-01	TCGA-DU-5872-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	55	52			ENST00000393045.2:c.1702C>G	p.His568Asp	p.H568D	ENST00000393045	NM_006099.3	568	Cac/Gac	0	0.637	GACCCCTTCTCACTTTCTGGG
FAM161A	84140	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	62067511	62067511	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-DU-5872-01	TCGA-DU-5872-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	118	68			ENST00000404929.1:c.628G>T	p.Asp210Tyr	p.D210Y	ENST00000404929	NM_001201543.1	210	Gat/Tat	0	0.408	CGAATATAATCCTCAACACAA
BUB1	699	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	111423902	111423902	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-DU-5872-01	TCGA-DU-5872-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	25	12			ENST00000302759.6:c.895A>G	p.Lys299Glu	p.K299E	ENST00000302759	NM_004336.4	299	Aag/Gag	0	0.428	TGATGCAACTTCTTATGAAGT
WDR33	55339	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	128522748	128522748	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G			TCGA-DU-5872-01	TCGA-DU-5872-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	13	13			ENST00000322313.4:c.474G>C	p.Gln158His	p.Q158H	ENST00000322313	NM_018383.4	158	caG/caC	0	0.398	TTATCATTACCTGTAATATTG
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-DU-5872-01	TCGA-DU-5872-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47	32			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
SPP2	6694	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	234969077	234969077	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-5872-01	TCGA-DU-5872-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40	23			ENST00000168148.3:c.398G>A	p.Arg133His	p.R133H	ENST00000168148	NM_006944.2	133	cGc/cAc	0	0.577	GTGCATGCTCGCTGCAGCTGG
HDAC4	9759	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	239976491	239976491	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DU-5872-01	TCGA-DU-5872-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	70	37			ENST00000345617.3:c.3027C>T	p.Pro1009=	p.P1009=	ENST00000345617	NM_006037.3	1009	ccC/ccT	0	0.507	CGTTTGCATTGGGTCTTTGCT
PROS1	5627	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	93624931	93624931	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-DU-5872-01	TCGA-DU-5872-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	107	69			ENST00000394236.3:c.403A>G	p.Lys135Glu	p.K135E	ENST00000394236	NM_000313.3	135	Aaa/Gaa	0	0.408	TTTCCATCTTTGCAGCTCATA
PLCH1	23007	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	155200741	155200741	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-DU-5872-01	TCGA-DU-5872-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	53	28			ENST00000340059.7:c.3098T>C	p.Leu1033Pro	p.L1033P	ENST00000340059	NM_001130960.1	1033	cTc/cCc	0	0.453	ATCTTTGTGGAGCAGAGCACT
SPATA16	83893	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	172631478	172631478	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-DU-5872-01	TCGA-DU-5872-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40	26			ENST00000351008.3:c.1560T>C	p.Asn520=	p.N520=	ENST00000351008	NM_031955.5	520	aaT/aaC	0	0.373	ACACACGTTCATTATTGTTTC
TRRAP	8295	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	98545941	98545941	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-5872-01	TCGA-DU-5872-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84	34			ENST00000359863.4:c.4625C>T	p.Thr1542Met	p.T1542M	ENST00000359863	NM_001244580.1	1542	aCg/aTg	0	0.498	GTCATGAAAACGGAGCGGGCG
CRYGN	155051	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	151135095	151135095	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148445096		TCGA-DU-5872-01	TCGA-DU-5872-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	34	27			ENST00000337323.2:c.257G>A	p.Arg86Gln	p.R86Q	ENST00000337323	NM_144727.1	86	cGg/cAg	0	0.627	TCCTACAGGCCGACAGGAGCC
CA9	768	hgsc.bcm.edu;ucsc.edu	GRCh37	9	35674208	35674208	+	synonymous_variant	Silent	SNP	T	T	C	rs137897809	by1000genomes	TCGA-DU-5872-01	TCGA-DU-5872-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15	7			ENST00000378357.4:c.252T>C	p.Pro84=	p.P84=	ENST00000378357	NM_001216.2	84	ccT/ccC	0	0.542	AGGATCTACCTGGAGAGGAGG
RORB	6096	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	77257427	77257427	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-DU-5872-01	TCGA-DU-5872-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	38	11			ENST00000376896.3:c.333G>C	p.Gln111His	p.Q111H	ENST00000376896	NM_006914.3	111	caG/caC	0	0.592	ggcagcagcagAGTGGGGAGG
SETX	23064	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	135205145	135205145	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-DU-5872-01	TCGA-DU-5872-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	38	28			ENST00000224140.5:c.1840A>G	p.Ile614Val	p.I614V	ENST00000224140	NM_015046.5	614	Atc/Gtc	0	0.353	GCAGGAGAGATTTTACATGCA
CCDC160	347475	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	133379653	133379653	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-5872-01	TCGA-DU-5872-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	13	9			ENST00000517294.1:c.823C>T	p.Arg275Cys	p.R275C	ENST00000517294		275	Cgc/Tgc	0	0.383	GGCAAAGATCCGCGGAGAGCT
PLXNA3	55558	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	153688767	153688767	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs142949704		TCGA-DU-5872-01	TCGA-DU-5872-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15	10			ENST00000369682.3:c.244A>G	p.Ser82Gly	p.S82G	ENST00000369682	NM_017514.3	82	Agc/Ggc	0	0.672	CCCGCCCCCCAGCATGCGCGT
ZNF451	26036	broad.mit.edu;ucsc.edu	GRCh37	6	57012701	57012701	+	stop_gained	Nonsense_Mutation	SNP	G	G	A			TCGA-DU-5872-01	TCGA-DU-5872-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58	40			ENST00000370706.4:c.1818G>A	p.Trp606Ter	p.W606*	ENST00000370706	NM_001031623.2	606	tgG/tgA	0	0.418	GGGGTAAATGGCAATGCCGGA
CPO	130749	broad.mit.edu;ucsc.edu	GRCh37	2	207814342	207814342	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C			TCGA-DU-5872-01	TCGA-DU-5872-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41	25			ENST00000272852.3:c.70T>C	p.Ser24Pro	p.S24P	ENST00000272852	NM_173077.2	24	Tcc/Ccc	0	0.473	CCTTTGCAGATCCTTAGCCCA
AKAP4	8852	broad.mit.edu;ucsc.edu	GRCh37	X	49957597	49957597	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-DU-5872-01	TCGA-DU-5872-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	66	31			ENST00000358526.2:c.1767T>C	p.Gly589=	p.G589=	ENST00000358526	NM_003886.2	589	ggT/ggC	0	0.488	CACTTTGGCCACCTCCACACT
ATRX	546	broad.mit.edu;ucsc.edu	GRCh37	X	76813106	76813106	+	missense_variant	Missense_Mutation	SNP	T	T	G			TCGA-DU-5872-01	TCGA-DU-5872-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	65	35			ENST00000373344.5:c.6515A>C	p.Glu2172Ala	p.E2172A	ENST00000373344	NM_000489.3	2172	gAa/gCa	0	0.338	AATCTTATCTTCCATGGTTCC
COL1A2	1278	broad.mit.edu;ucsc.edu	GRCh37	7	94057712	94057712	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-5872-01	TCGA-DU-5872-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	100	34			ENST00000297268.6:c.3634C>T	p.Pro1212Ser	p.P1212S	ENST00000297268	NM_000089.3	1212	Cca/Tca	0	0.488	TGAAAACATCCCAGCCAAGAA
SLCO1B1	10599	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	21329781	21329781	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-DU-6401-01	TCGA-DU-6401-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	43	39			ENST00000256958.2:c.431T>C	p.Ile144Thr	p.I144T	ENST00000256958	NM_006446.4	144	aTt/aCt	0	0.274	ACTTGTTTAATTAATCAAATT
DYNC1H1	1778	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	14	102508452	102508452	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-DU-6401-01	TCGA-DU-6401-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18	12			ENST00000360184.4:c.12205A>G	p.Ile4069Val	p.I4069V	ENST00000360184	NM_001376.4	4069	Att/Gtt	0	0.537	GATCACTTCAATTGCAATCGG
ITGAD	3681	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	31419095	31419095	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-DU-6401-01	TCGA-DU-6401-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21	17			ENST00000389202.2:c.867C>T	p.His289=	p.H289=	ENST00000389202	NM_005353.2	289	caC/caT	0	0.617	AGGTGGGACACGCTTTCCAGG
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-6401-01	TCGA-DU-6401-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8	20			ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	0	0.522	ATCTCGAAGCGCTCACGCCCA
TMC6	11322	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	76116777	76116777	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-6401-01	TCGA-DU-6401-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	109	29			ENST00000590602.1:c.1672G>A	p.Val558Ile	p.V558I	ENST00000590602		558	Gtc/Atc	0	0.637	AACATGAGGACGAAGTCCATC
CEACAM5	1048	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	42224879	42224879	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DU-6401-01	TCGA-DU-6401-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69	45			ENST00000221992.6:c.1809G>A	p.Ser603=	p.S603=	ENST00000221992	NM_004363.2	603	tcG/tcA	0	0.547	CCCCAGACTCGTCTTACCTTT
DHDDS	79947	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	26772898	26772898	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-6401-01	TCGA-DU-6401-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	92	46			ENST00000360009.2:c.415G>A	p.Val139Ile	p.V139I	ENST00000360009	NM_024887.3	139	Gta/Ata	0	0.517	TGCACAAGCTGTACAGGCCAC
CELSR1	9620	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	22	46929726	46929726	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-DU-6401-01	TCGA-DU-6401-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	103	82			ENST00000262738.3:c.3342C>G	p.Asn1114Lys	p.N1114K	ENST00000262738	NM_014246.1	1114	aaC/aaG	0	0.592	TGTTGGACTTGTTGGTGACAT
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913499		TCGA-DU-6401-01	TCGA-DU-6401-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	53	28			ENST00000345146.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000345146	NM_005896.2	132	Cgt/Agt	0	0.398	TAAGCATGACGACCTATGATG
SLIT2	9353	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	20490510	20490510	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-6401-01	TCGA-DU-6401-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	180	35			ENST00000504154.1:c.680G>A	p.Arg227Lys	p.R227K	ENST00000504154	NM_004787.1	227	aGg/aAg	0	0.498	CTTCGCCAAAGGCCTCGGGTT
LAMA2	3908	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	129419503	129419503	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-DU-6401-01	TCGA-DU-6401-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64	9			ENST00000421865.2:c.582T>C	p.Asp194=	p.D194=	ENST00000421865	NM_001079823.1	194	gaT/gaC	0	0.443	ATGCCAAAGATGATGAGGTCA
TNFAIP3	7128	hgsc.bcm.edu;broad.mit.edu	GRCh37	6	138199814	138199814	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-6401-01	TCGA-DU-6401-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84	7			ENST00000237289.4:c.1232G>A	p.Arg411Gln	p.R411Q	ENST00000237289	NM_001270507.1	411	cGg/cAg	0	0.557	TCAGAGAGGCGGCAAAAGAAT
ENPP2	5168	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	120596283	120596283	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-DU-6401-01	TCGA-DU-6401-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	63	66			ENST00000259486.6:c.1530T>C	p.Pro510=	p.P510=	ENST00000259486	NM_006209.4	510	ccT/ccC	0	0.348	AAACATCCAAAGGTTTCCTAA
KCNT1	57582	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	138657002	138657002	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-DU-6401-01	TCGA-DU-6401-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98	11			ENST00000371757.2:c.1161G>T	p.Met387Ile	p.M387I	ENST00000371757	NM_020822.2	387	atG/atT	0	0.642	ACCTTCTCATGGACTTCCTGA
CXorf23	256643	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	19983583	19983583	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-DU-6401-01	TCGA-DU-6401-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36	41			ENST00000379687.3:c.853C>A	p.Arg285Ser	p.R285S	ENST00000379687	NM_198279.3	285	Cgt/Agt	0	0.458	AGCTTAGGACGTTTGTGACGA
HDAC6	10013	hgsc.bcm.edu;broad.mit.edu	GRCh37	X	48682452	48682452	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-DU-6401-01	TCGA-DU-6401-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	50	6			ENST00000334136.5:c.3424A>G	p.Asn1142Asp	p.N1142D	ENST00000334136		1142	Aat/Gat	0	0.592	AATCCAAGAGAATTGGGTGTG
GLUD2	2747	hgsc.bcm.edu;broad.mit.edu	GRCh37	X	120182836	120182836	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-6401-01	TCGA-DU-6401-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	214	22			ENST00000328078.1:c.1298G>A	p.Gly433Glu	p.G433E	ENST00000328078	NM_012084.3	433	gGa/gAa	0	0.418	TTGAATGCTGGAGGAGTGACA
ZFYVE26	23503	broad.mit.edu;ucsc.edu	GRCh37	14	68251787	68251787	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-6401-01	TCGA-DU-6401-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	111	75			ENST00000347230.4:c.3512G>A	p.Ser1171Asn	p.S1171N	ENST00000347230	NM_015346.3	1171	aGc/aAc	0	0.502	AGGCTCAGAGCTCAAACTTTG
MAP2K3	5606	broad.mit.edu;ucsc.edu	GRCh37	17	21217496	21217496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35755743		TCGA-DU-6401-01	TCGA-DU-6401-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	317	65			ENST00000342679.4:c.998C>T	p.Thr333Met	p.T333M	ENST00000342679	NM_145109.2	333	aCg/aTg	0	0.617	ACCAAGAAGACGGACATTGCT
LPAR4	2846	broad.mit.edu;ucsc.edu	GRCh37	X	78010568	78010568	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-DU-6401-01	TCGA-DU-6401-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	260	50			ENST00000435339.3:c.202A>G	p.Met68Val	p.M68V	ENST00000435339	NM_005296.2	68	Atg/Gtg	0	0.358	CTGTTTCCGCATGAAAATGAG
PTCD1	26024	broad.mit.edu;ucsc.edu	GRCh37	7	99026819	99026819	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DU-6401-01	TCGA-DU-6401-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	92	10			ENST00000413834.1:c.969C>T	p.Ile323=	p.I323=	ENST00000413834		323	atC/atT	0	0.557	GCCCTTTGTGGATGATTTCCT
XPO6	23214	broad.mit.edu;ucsc.edu	GRCh37	16	28137080	28137080	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-6401-01	TCGA-DU-6401-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	117	29			ENST00000304658.5:c.1696C>T	p.Arg566Cys	p.R566C	ENST00000304658	NM_015171.3	566	Cgc/Tgc	0	0.582	TCGGCCAGGCGGCCCACGGCC
ESCO2	157570	broad.mit.edu;hgsc.bcm.edu	GRCh37	8	27634263	27634266	+	frameshift_variant	Frame_Shift_Del	DEL	TAAG	TAAG	-			TCGA-DU-6401-01	TCGA-DU-6401-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	38	23			ENST00000305188.8:c.440_443delAGTA	p.Lys147IlefsTer23	p.K147Ifs*23	ENST00000305188	NM_001017420.2	146	gcTAAG/gc	0	0.353	GTTTAACTGCTAAGTATCAACCAA
ATRX	546	broad.mit.edu;hgsc.bcm.edu	GRCh37	X	76939673	76939674	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T			TCGA-DU-6401-01	TCGA-DU-6401-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	94	52			ENST00000373344.5:c.1074dupA	p.Leu359ThrfsTer3	p.L359Tfs*3	ENST00000373344	NM_000489.3	358	-/A	0	0.366	GTCTCAATCAGTTTTTTTGCCT
ANK3	288	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	61958113	61958113	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	19	14			ENST00000280772.2:c.1674A>G	p.Leu558=	p.L558=	ENST00000280772	NM_020987.3	558	ttA/ttG	0	0.498	TTGTTATAGATAAAGACGCTC
OR2AG2	338755	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	6789589	6789589	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18	10			ENST00000338569.2:c.600C>T	p.Tyr200=	p.Y200=	ENST00000338569	NM_001004490.1	200	taC/taT	0	0.493	CACCTGTCACGTATATTATAA
SIPA1	6494	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	65408733	65408733	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	105	67			ENST00000394224.3:c.341G>A	p.Arg114Gln	p.R114Q	ENST00000394224	NM_153253.29	114	cGa/cAa	0	0.632	CTTGAGCCTCGATGGTTTGCC
PLEKHA5	54477	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	19489486	19489486	+	missense_variant	Missense_Mutation	SNP	A	A	C			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40	26			ENST00000429027.2:c.2486A>C	p.Glu829Ala	p.E829A	ENST00000429027	NM_001256470.1	829	gAa/gCa	0	0.348	GATAAGTTAGAATACGATGTA
LRRK1	79705	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	101588788	101588788	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35	58			ENST00000388948.3:c.3225A>G	p.Thr1075=	p.T1075=	ENST00000388948	NM_024652.3	1075	acA/acG	0	0.448	GCTGTAGCACATTCAGAGTGA
TP53	7157	hgsc.bcm.edu;broad.mit.edu	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343		TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0	9			ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	0	0.542	GCACAAACACGCACCTCAAAG
GAS2L2	246176	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	34079638	34079638	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	38	23			ENST00000254466.6:c.232G>A	p.Ala78Thr	p.A78T	ENST00000254466	NM_139285.3	78	Gcc/Acc	0	0.652	GCCAGGAAGGCCAGGGCAGCG
HELZ	9931	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	65174991	65174991	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37	17			ENST00000358691.5:c.1214G>A	p.Arg405His	p.R405H	ENST00000358691	NM_014877.3	405	cGt/cAt	0	0.348	AGAATCCCAACGTTTAGCTGT
EPS15L1	58513	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	16487940	16487940	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23	15			ENST00000455140.2:c.2373G>A	p.Pro791=	p.P791=	ENST00000455140	NM_001258374.1	791	ccG/ccA	0	0.612	GACCGCTGGGCGGTTTAGGCC
FGR	2268	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	27943402	27943402	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	141	70			ENST00000374005.3:c.648C>T	p.Phe216=	p.F216=	ENST00000374005	NM_005248.2	216	ttC/ttT	0	0.562	GCACCGAGTTGAACTGAACCC
ZSCAN20	7579	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	33960425	33960425	+	synonymous_variant	Silent	SNP	T	T	G			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	154	93			ENST00000361328.3:c.2481T>G	p.Pro827=	p.P827=	ENST00000361328	NM_145238.3	827	ccT/ccG	0	0.448	GTAGTGAGCCTGGGGGAAACT
LRRC8D	55144	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	90400076	90400076	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	34	13			ENST00000337338.5:c.1449C>T	p.Pro483=	p.P483=	ENST00000337338	NM_001134479.1	483	ccC/ccT	0	0.468	CGGGGGTGCCCGATGCTGTCT
CFHR5	81494	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	196953247	196953247	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	49	21			ENST00000256785.4:c.410C>T	p.Pro137Leu	p.P137L	ENST00000256785		137	cCt/cTt	0	0.348	TGGTCCACTCCTCCCATATGC
ASPM	259266	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	197091601	197091601	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	25	11			ENST00000367409.4:c.3515C>T	p.Thr1172Met	p.T1172M	ENST00000367409	NM_018136.4	1172	aCg/aTg	0	0.413	ACCAGTTTGCGTACATTCCAC
SLC25A1	6576	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	22	19164192	19164192	+	missense_variant	Missense_Mutation	SNP	T	T	G			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26	12			ENST00000215882.5:c.646A>C	p.Lys216Gln	p.K216Q	ENST00000215882	NM_005984.3	216	Aag/Cag	0	0.592	TTCATGGGCTTGTTGGGGTTG
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	56	35			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
VIL1	7429	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	219295519	219295519	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47	19			ENST00000248444.5:c.1020C>T	p.Ala340=	p.A340=	ENST00000248444	NM_007127.2	340	gcC/gcT	0	0.597	CTGAGTCGGCCGTCTTTCAGC
PCDHA11	56138	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	140249016	140249016	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	171	147			ENST00000398640.2:c.328G>A	p.Val110Met	p.V110M	ENST00000398640	NM_018902.3	110	Gtg/Atg	0	0.552	GGAGGTGATCGTGGACAGGCC
DUSP22	56940	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	348774	348774	+	synonymous_variant	Silent	SNP	G	G	T			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	103	24			ENST00000344450.5:c.441G>T	p.Arg147=	p.R147=	ENST00000344450	NM_020185.3	147	cgG/cgT	0	0.522	TCCAGTATCGGCAGTGGCTGA
FIGNL1	63979	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	50513534	50513534	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84	50			ENST00000419119.1:c.1452A>G	p.Ala484=	p.A484=	ENST00000419119		484	gcA/gcG	0	0.443	CAGCAAACAATGCACGGACCA
ZNF138	7697	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	64292367	64292367	+	missense_variant	Missense_Mutation	SNP	A	A	C			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	19	16			ENST00000440155.2:c.669A>C	p.Lys223Asn	p.K223N	ENST00000440155	NM_006524.3	223	aaA/aaC	0	0.368	CTGGAGAAAAACCCTATAAAT
SEMA3C	10512	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	80374454	80374454	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39	24			ENST00000265361.3:c.2012C>T	p.Thr671Met	p.T671M	ENST00000265361	NM_006379.3	671	aCg/aTg	0	0.478	CCATTTGTCCGTCACAACAGC
JPH1	56704	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	75171665	75171665	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26	18			ENST00000342232.4:c.1213G>A	p.Ala405Thr	p.A405T	ENST00000342232	NM_020647.2	405	Gcg/Acg	0	0.607	ACAGCTCTCGCGATGTCGCAC
NUDCD1	84955	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	110287672	110287672	+	missense_variant	Missense_Mutation	SNP	A	A	C			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	31	11			ENST00000239690.4:c.1082T>G	p.Val361Gly	p.V361G	ENST00000239690	NM_032869.3	361	gTa/gGa	0	0.383	ATCTCCAATTACTAGCTCTGG
EPPK1	83481	hgsc.bcm.edu;broad.mit.edu	GRCh37	8	144940576	144940576	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73	4			ENST00000525985.1:c.6846G>A	p.Ser2282=	p.S2282=	ENST00000525985	NM_031308.2	2282	tcG/tcA	0	0.736	CCTCCTCCACCGACAGCCTCA
ZFP37	7539	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	115811700	115811700	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7	27			ENST00000374227.3:c.291A>G	p.Arg97=	p.R97=	ENST00000374227		97	agA/agG	0	0.403	CTTGACTGGGTCTTTTCCCCT
DDX31	64794	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	135522404	135522404	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	60	40			ENST00000372159.3:c.1324A>G	p.Ser442Gly	p.S442G	ENST00000372159	NM_022779.7	442	Agt/Ggt	0	0.493	ACAGAAATACTGACTGGATCA
GSPT2	23708	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	51488448	51488448	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24	24			ENST00000340438.4:c.1726G>A	p.Val576Met	p.V576M	ENST00000340438	NM_018094.4	576	Gtg/Atg	0	0.418	ACCCCGCTTCGTGAAACAAGA
ZCCHC5	203430	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	77912924	77912924	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23	9			ENST00000321110.1:c.994C>A	p.Leu332Ile	p.L332I	ENST00000321110	NM_152694.2	332	Ctc/Atc	0	0.463	CCTTGGCAGAGTTGATGGATG
TENM1	10178	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	123525932	123525932	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8	15			ENST00000422452.2:c.5658G>A	p.Gly1886=	p.G1886=	ENST00000422452	NM_001163279.1	1886	ggG/ggA	0	0.378	TCCAAATTTTCCCATCAGCCC
KCNJ8	3764	broad.mit.edu;ucsc.edu	GRCh37	12	21926252	21926252	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37	34			ENST00000240662.2:c.299A>G	p.Asp100Gly	p.D100G	ENST00000240662	NM_004982.3	100	gAc/gGc	0	0.507	AGCATAGATGTCCCCATGGGC
SMARCA4	6597	broad.mit.edu;ucsc.edu	GRCh37	19	11132434	11132434	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	19	14			ENST00000344626.4:c.2650C>A	p.His884Asn	p.H884N	ENST00000344626	NM_003072.3	884	Cac/Aac	0	0.622	GGACGAAGGTCACCGCATGAA
PCDH18	54510	broad.mit.edu;ucsc.edu	GRCh37	4	138452008	138452008	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26	3			ENST00000344876.4:c.1235A>G	p.Glu412Gly	p.E412G	ENST00000344876	NM_019035.3	412	gAa/gGa	0	0.403	ATAATTGTTTTCATATGTCTT
RBM41	55285	broad.mit.edu;hgsc.bcm.edu	GRCh37	X	106331986	106331986	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-			TCGA-HT-7606-01	TCGA-HT-7606-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26	15			ENST00000372479.3:c.607delG	p.Glu203LysfsTer6	p.E203Kfs*6	ENST00000372479	NM_018301.3	203	Gaa/aa	0	0.428	TGAAACTCTTCAAGACGTTTT
ARMC3	219681	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	23292319	23292319	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73	59			ENST00000298032.5:c.1707C>T	p.Asn569=	p.N569=	ENST00000298032	NM_173081.3	569	aaC/aaT	0	0.323	ACATAATTAACGATGGATTCT
ATG16L2	89849	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	72528829	72528829	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40	15			ENST00000321297.5:c.247G>C	p.Val83Leu	p.V83L	ENST00000321297	NM_033388.1	83	Gtc/Ctc	0	0.587	CTCAGACCAAGTCCCATCACT
BCL9L	283149	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	118772576	118772576	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29	14			ENST00000334801.3:c.1876A>G	p.Met626Val	p.M626V	ENST00000334801	NM_182557.2	626	Atg/Gtg	0	0.622	ATGGCATTCATGGGCACCTCC
WNK1	65125	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	994382	994382	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	86	29			ENST00000315939.6:c.4412C>T	p.Pro1471Leu	p.P1471L	ENST00000315939	NM_018979.3	1471	cCt/cTt	0	0.507	GGTCCTAAGCCTCCAGCTGTA
PSMC6	5706	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	14	53175072	53175072	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21	25			ENST00000445930.2:c.173A>G	p.Glu58Gly	p.E58G	ENST00000445930		58	gAa/gGa	0	0.353	GAAAAGTCTGAAAATGATCTG
COPS2	9318	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	49447771	49447771	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	56	49			ENST00000299259.6:c.5C>G	p.Ser2Cys	p.S2C	ENST00000299259		2	tCt/tGt	0	0.557	CTCCATGTCAGACATCTTGGC
PDE8A	5151	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	85610300	85610300	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41	45			ENST00000310298.4:c.299G>A	p.Cys100Tyr	p.C100Y	ENST00000310298		100	tGt/tAt	0	0.383	TGCAGGGCATGTGAAAAAGCA
DHX38	9785	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	72132924	72132924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148934675		TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36	20			ENST00000268482.3:c.863C>T	p.Pro288Leu	p.P288L	ENST00000268482	NM_014003.3	288	cCg/cTg	0	0.617	GGGTCCACCCCGCGTCTGTCC
ZFHX3	463	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	72993684	72993684	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	117	23			ENST00000268489.5:c.361G>T	p.Asp121Tyr	p.D121Y	ENST00000268489	NM_006885.3	121	Gac/Tac	0	0.687	CTCTCCTCGTCCCCCTCCTCA
PLCG2	5336	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	81953235	81953235	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	72	28			ENST00000359376.3:c.2201C>A	p.Pro734His	p.P734H	ENST00000359376	NM_002661.3	734	cCc/cAc	0	0.517	CTGCGCTACCCCGTGACCCCC
METTL16	79066	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	2324130	2324130	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	237	104			ENST00000263092.6:c.957C>T	p.Ser319=	p.S319=	ENST00000263092	NM_024086.3	319	tcC/tcT	0	0.453	CCTTCATCACGGACGCCAGCA
ALDH4A1	8659	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	19209803	19209803	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97	21			ENST00000375341.3:c.573C>T	p.Ser191=	p.S191=	ENST00000375341	NM_003748.3	191	agC/agT	0	0.647	TGCTGTTGGTGCTCGGGGGCA
ALDH4A1	8659	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	19209838	19209838	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69	24			ENST00000375341.3:c.538C>G	p.Leu180Val	p.L180V	ENST00000375341	NM_003748.3	180	Ctg/Gtg	0	0.642	TGCCCCTCCAGCTCCACCGCA
TMEM39B	55116	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	32542835	32542835	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	187	19			ENST00000336294.5:c.506C>T	p.Thr169Met	p.T169M	ENST00000336294	NM_018056.2	169	aCg/aTg	0	0.592	ACCGTTCTCACGGCAACAGGC
TOR1AIP1	26092	hgsc.bcm.edu;ucsc.edu	GRCh37	1	179876983	179876983	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	38	4			ENST00000606911.2:c.822G>C	p.Lys274Asn	p.K274N	ENST00000606911		274	aaG/aaC	0	0.328	CTCATGATAAGCAACCTTCAG
BRINP3	339479	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	190067492	190067492	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	59	38			ENST00000367462.3:c.1957G>A	p.Asp653Asn	p.D653N	ENST00000367462	NM_199051.1	653	Gac/Aac	0	0.428	CGGGAAGGGTCAATAAACTCC
HSPA13	6782	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	21	15748040	15748040	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	116	37			ENST00000285667.3:c.681C>T	p.Gly227=	p.G227=	ENST00000285667	NM_006948.4	227	ggC/ggT	0	0.483	GAGTTCCTCCGCCCAAGTCTA
BCR	613	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	22	23631729	23631729	+	synonymous_variant	Silent	SNP	C	C	G			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36	24			ENST00000305877.8:c.2628C>G	p.Ser876=	p.S876=	ENST00000305877	NM_004327.3	876	tcC/tcG	0	0.572	CCCTGACATCCGTGGAGCTGC
LRP1B	53353	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	141274478	141274478	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97	35			ENST00000389484.3:c.8129G>C	p.Gly2710Ala	p.G2710A	ENST00000389484	NM_018557.2	2710	gGa/gCa	0	0.328	TTCATCACGTCCATCCTCACA
DNAH7	56171	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	196877622	196877622	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26	20			ENST00000312428.6:c.878G>A	p.Arg293His	p.R293H	ENST00000312428	NM_018897.2	293	cGt/cAt	0	0.279	ATCAACTAAACGTAATTTTCT
CACNA1D	776	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	53837571	53837571	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	215	97			ENST00000288139.4:c.5617G>C	p.Glu1873Gln	p.E1873Q	ENST00000288139	NM_000720.3	1873	Gag/Cag	0	0.617	GGAATGCTACGAGGATGACAG
SLITRK3	22865	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	164906713	164906713	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	34	11			ENST00000475390.1:c.1906C>A	p.Pro636Thr	p.P636T	ENST00000475390		636	Cca/Aca	0	0.527	GCACTGGTTGGTGCCCCAATA
GABRA1	2554	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	161324195	161324195	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	138	44			ENST00000428797.2:c.1138G>C	p.Ala380Pro	p.A380P	ENST00000428797	NM_001127643.1	380	Gcc/Ccc	0	0.458	CCCTAATTTGGCCAGGGGCGA
EGFR	1956	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	55211008	55211008	+	missense_variant	Missense_Mutation	SNP	A	A	T			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90	32			ENST00000275493.2:c.251A>T	p.Glu84Val	p.E84V	ENST00000275493	NM_005228.3	84	gAg/gTg	0	0.448	ACCATCCAGGAGGTGGCTGGT
SEMA3E	9723	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	83119551	83119551	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	59	20			ENST00000307792.3:c.155C>A	p.Pro52His	p.P52H	ENST00000307792	NM_012431.2	52	cCt/cAt	0	0.413	AAATCCAAAAGGGCTATGAAA
RNF19A	25897	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	101287238	101287238	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	77	27			ENST00000519449.1:c.826C>T	p.Arg276Cys	p.R276C	ENST00000519449	NM_015435.4	276	Cgt/Tgt	0	0.418	GTTCTCAAACGTAAGCTCTGG
SLC45A4	57210	hgsc.bcm.edu;broad.mit.edu	GRCh37	8	142231748	142231748	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88	6			ENST00000024061.3:c.205C>T	p.Arg69Trp	p.R69W	ENST00000024061	NM_001080431.1	69	Cgg/Tgg	0	0.617	ATGAAGGGCCGCCGGCGGCCC
EPPK1	83481	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	144945911	144945911	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17	8			ENST00000525985.1:c.1511G>A	p.Arg504Gln	p.R504Q	ENST00000525985	NM_031308.2	504	cGg/cAg	0	0.677	GGGCCGGCCCCGGAACTTCCC
APBA1	320	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	72131516	72131516	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17	15			ENST00000265381.4:c.611C>A	p.Ala204Glu	p.A204E	ENST00000265381	NM_001163.3	204	gCg/gAg	0	0.721	CAGCTCGGGCGCGTCCCCTAT
APOO	79135	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	23899066	23899066	+	missense_variant	Missense_Mutation	SNP	T	T	A			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47	36			ENST00000379226.4:c.13A>T	p.Ile5Phe	p.I5F	ENST00000379226	NM_024122.4	5	Att/Ttt	0	0.478	GACCTCTGAATTACCTGAAAT
HLTF	6596	broad.mit.edu;ucsc.edu	GRCh37	3	148792096	148792096	+	synonymous_variant	Silent	SNP	A	A	C			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23	34			ENST00000310053.5:c.435T>G	p.Pro145=	p.P145=	ENST00000310053	NM_003071.3	145	ccT/ccG	0	0.363	TCATATGCAGAGGCATGGTAA
LUZP4	51213	broad.mit.edu;ucsc.edu	GRCh37	X	114541268	114541268	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	114	23			ENST00000371920.3:c.841G>A	p.Val281Met	p.V281M	ENST00000371920	NM_016383.3	281	Gtg/Atg	0	0.428	GAGAGATCTCGTGGCCACTGA
PGM3	5238	broad.mit.edu;ucsc.edu	GRCh37	6	83884095	83884095	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7	3			ENST00000506587.1:c.1324C>A	p.Gln442Lys	p.Q442K	ENST00000506587	NM_001199917.1	442	Cag/Aag	0	0.383	GTTCTGACCTGGTTAAACAAG
KIF1B	23095	broad.mit.edu;ucsc.edu	GRCh37	1	10386237	10386237	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	250	21			ENST00000263934.6:c.2606C>T	p.Thr869Met	p.T869M	ENST00000263934	NM_015074.3	869	aCg/aTg	0	0.572	ACTTTTTCCACGGCCGATTCC
DNAH11	8701	broad.mit.edu;ucsc.edu	GRCh37	7	21640450	21640450	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	160	57			ENST00000328843.6:c.3157C>T	p.Leu1053Phe	p.L1053F	ENST00000328843		1053	Ctc/Ttc	0	0.438	GAAGCATTTTCTCTTGTATGG
KIF19	124602	broad.mit.edu;ucsc.edu	GRCh37	17	72343952	72343952	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8	3			ENST00000389916.4:c.961G>A	p.Ala321Thr	p.A321T	ENST00000389916	NM_153209.3	321	Gct/Act	0	0.627	AGTGATGATCGCTCACATCAG
DCAF12L1	139170	broad.mit.edu;ucsc.edu	GRCh37	X	125686452	125686452	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	54	21			ENST00000371126.1:c.140C>T	p.Thr47Met	p.T47M	ENST00000371126	NM_178470.4	47	aCg/aTg	0	0.721	CGAGCGATACGTCGCCGGCCG
PTEN	5728	broad.mit.edu;hgsc.bcm.edu	GRCh37	10	89717715	89717716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A			TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	56	48			ENST00000371953.3:c.741dupA	p.Pro248ThrfsTer5	p.P248Tfs*5	ENST00000371953	NM_000314.4	247	tta/ttAa	0	0.406	CCTCAGCCGTTACCTGTGTGTG
BACH1	571	broad.mit.edu;hgsc.bcm.edu	GRCh37	21	30699512	30699513	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	rs145991657		TCGA-DU-8158-01	TCGA-DU-8158-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52	29			ENST00000399921.1:c.1367_1368delTA	p.Leu456Ter	p.L456*	ENST00000399921	NM_206866.1	456	tTA/t	0	0.436	TTCACAACATTAAGTTCTGTCA
CUBN	8029	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	16990512	16990512	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62	15			ENST00000377833.4:c.5174G>C	p.Gly1725Ala	p.G1725A	ENST00000377833	NM_001081.3	1725	gGg/gCg	0	0.512	GTGGAAACCCCCAGCACTGAT
OR52E8	390079	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	5878264	5878264	+	stop_gained	Nonsense_Mutation	SNP	A	A	C			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28	12			ENST00000537935.1:c.669T>G	p.Tyr223Ter	p.Y223*	ENST00000537935	NM_001005168.1	223	taT/taG	0	0.463	GGATCCTGACATAGGAGAGAA
LRP4	4038	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	46893136	46893136	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	19	18			ENST00000378623.1:c.4632C>T	p.Leu1544=	p.L1544=	ENST00000378623	NM_002334.3	1544	ctC/ctT	0	0.557	GTTTCCCATTGAGGTCAGCAC
HTR3B	9177	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	113803068	113803068	+	synonymous_variant	Silent	SNP	C	C	A			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	192	19			ENST00000260191.2:c.426C>A	p.Thr142=	p.T142=	ENST00000260191	NM_006028.4	142	acC/acA	0	0.433	CATCTGGGACCATTGAGAACT
SNX19	399979	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	130750571	130750571	+	stop_gained	Nonsense_Mutation	SNP	G	G	A			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	263	52			ENST00000265909.4:c.2704C>T	p.Gln902Ter	p.Q902*	ENST00000265909	NM_014758.2	902	Cag/Tag	0	0.517	GCCAGTTTCTGCTCTTGGGTC
HMGA2	8091	hgsc.bcm.edu;broad.mit.edu	GRCh37	12	66221789	66221789	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71	5			ENST00000403681.2:c.120C>T	p.Thr40=	p.T40=	ENST00000403681	NM_003483.4	40	acC/acT	0	0.448	AGGAACCAACCGGTGAGCCCT
PTPRB	5787	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	70954486	70954486	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	65	9			ENST00000334414.6:c.4397A>G	p.Asp1466Gly	p.D1466G	ENST00000334414	NM_001109754.2	1466	gAt/gGt	0	0.512	ATTGCTGAGATCTCCACTGTG
SHF	90525	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	45470424	45470424	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41	16			ENST00000290894.8:c.384A>G	p.Pro128=	p.P128=	ENST00000290894	NM_138356.2	128	ccA/ccG	0	0.567	GGACCTTCTCTGGGGCTCCTG
RHBDF1	64285	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	111434	111434	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	56	7			ENST00000262316.6:c.1344C>T	p.Tyr448=	p.Y448=	ENST00000262316	NM_022450.3	448	taC/taT	0	0.716	TGACGTTCTCGTAGACCCCGC
PRSS22	64063	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	2906139	2906139	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99	17			ENST00000161006.3:c.225C>T	p.Cys75=	p.C75=	ENST00000161006	NM_022119.3	75	tgC/tgT	0	0.617	GAGAACCTGCGCAGTGGTGGG
ERCC4	2072	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	14031642	14031642	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	55	22			ENST00000311895.7:c.1831G>A	p.Gly611Arg	p.G611R	ENST00000311895	NM_005236.2	611	Gga/Aga	0	0.363	TCTTATATACGGAGGTTCAAC
ANKRD11	29123	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	89348104	89348104	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	110	23			ENST00000301030.4:c.4846G>A	p.Gly1616Arg	p.G1616R	ENST00000301030	NM_001256183.1	1616	Gga/Aga	0	0.607	TTGGGGTCTCCGGACCGGTGC
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343		TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	13	28			ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	0	0.542	GCACAAACACGCACCTCAAAG
MYO19	80179	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	34866651	34866651	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	13	7			ENST00000431794.3:c.1091G>A	p.Arg364Gln	p.R364Q	ENST00000431794	NM_001163735.1	364	cGg/cAg	0	0.627	GCAGGGCTTCCGGAACACCTG
FCGBP	8857	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	40357728	40357728	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40	12			ENST00000221347.6:c.15585C>T	p.Ser5195=	p.S5195=	ENST00000221347	NM_003890.2	5195	agC/agT	0	0.587	AACAGCGCTCGCTGCAGTCTG
PPP1R12C	54776	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	55605714	55605714	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	135	27			ENST00000263433.3:c.1682A>C	p.Gln561Pro	p.Q561P	ENST00000263433	NM_017607.3	561	cAg/cCg	0	0.657	ACCCCACACCTGTGTGGACCT
AGL	178	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	100346642	100346642	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69	17			ENST00000294724.4:c.1910C>T	p.Ala637Val	p.A637V	ENST00000294724	NM_000028.2	637	gCg/gTg	0	0.353	CATAGATCAGCGTATGATGCT
CEPT1	10390	hgsc.bcm.edu;broad.mit.edu	GRCh37	1	111726868	111726868	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	121	6			ENST00000545121.1:c.1187C>T	p.Ala396Val	p.A396V	ENST00000545121	NM_001007794.1	396	gCg/gTg	0	0.398	AATCAGATTGCGTCTCACCTG
TCHH	7062	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	152080904	152080904	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs71585886		TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73	35			ENST00000368804.1:c.4789T>A	p.Phe1597Ile	p.F1597I	ENST00000368804	NM_007113.3	1597	Ttc/Atc	0	0.582	TCCTCCATGAATTTTCTCTCT
CFH	3075	hgsc.bcm.edu;broad.mit.edu	GRCh37	1	196642210	196642210	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	117	9			ENST00000367429.4:c.161C>A	p.Pro54His	p.P54H	ENST00000367429	NM_000186.3	54	cCt/cAt	0	0.403	AAATGCCGCCCTGGATATAGA
RYR2	6262	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	237872820	237872820	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	12	10			ENST00000366574.2:c.10183C>T	p.Leu3395Phe	p.L3395F	ENST00000366574	NM_001035.2	3395	Ctc/Ttc	0	0.418	AGCAGAGGAGCTCTTCCGCAT
ZNF638	27332	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	71590305	71590305	+	missense_variant	Missense_Mutation	SNP	A	A	C			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	51	26			ENST00000409544.1:c.1402A>C	p.Ile468Leu	p.I468L	ENST00000409544	NM_001252612.1	468	Atc/Ctc	0	0.264	GAATCCTGAGATCCTCCCATC
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913499		TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	107	34			ENST00000345146.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000345146	NM_005896.2	132	Cgt/Agt	0	0.398	TAAGCATGACGACCTATGATG
TRPM8	79054	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	234905020	234905020	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82	9			ENST00000324695.4:c.2990A>G	p.Gln997Arg	p.Q997R	ENST00000324695	NM_024080.4	997	cAg/cGg	0	0.537	TGGAAGTTCCAGAGGTACTTC
KCNH8	131096	hgsc.bcm.edu;broad.mit.edu	GRCh37	3	19575424	19575424	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52	5			ENST00000328405.2:c.3157G>T	p.Gly1053Cys	p.G1053C	ENST00000328405	NM_144633.2	1053	Ggc/Tgc	0	0.488	ATCAGAGGAGGGCAGCTTCAG
ABI3BP	25890	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	100489774	100489774	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	158	21			ENST00000284322.5:c.2421A>G	p.Gln807=	p.Q807=	ENST00000284322	NM_015429.3	807	caA/caG	0	0.468	TGTCAGGCTTTTGGATGTATC
GPR149	344758	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	154146852	154146852	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47	7			ENST00000389740.2:c.553G>A	p.Asp185Asn	p.D185N	ENST00000389740	NM_001038705.1	185	Gac/Aac	0	0.657	CTGGAGCAGTCCACCAGGCAG
STATH	6779	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	70866654	70866654	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	167	46			ENST00000246895.4:c.177A>G	p.Gln59=	p.Q59=	ENST00000246895	NM_003154.2	59	caA/caG	0	0.373	AATACCAACAATATACCTTTT
CAPSL	133690	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	35910530	35910530	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	89	18			ENST00000397367.2:c.253C>T	p.Arg85Trp	p.R85W	ENST00000397367	NM_144647.3	85	Cgg/Tgg	0	0.358	TCAAACCTCCGGAAAAGTTCT
SPOCK1	6695	hgsc.bcm.edu;ucsc.edu	GRCh37	5	136324179	136324179	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	139	46			ENST00000394945.1:c.860C>T	p.Ser287Leu	p.S287L	ENST00000394945	NM_004598.3	287	tCg/tTg	0	0.498	GGAGTCACACGAGTTGAAAAG
RNF145	153830	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	158621725	158621725	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	155	65			ENST00000518802.1:c.382A>G	p.Arg128Gly	p.R128G	ENST00000518802	NM_001199380.1	128	Agg/Ggg	0	0.363	TATTCTTACCTGGAAATTTGA
COL19A1	1310	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	70877920	70877920	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	101	15			ENST00000322773.4:c.2449A>G	p.Ile817Val	p.I817V	ENST00000322773	NM_001858.4	817	Att/Gtt	0	0.279	TCCTAAGGGTATTCCATTTAA
PRDM1	639	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	106555167	106555167	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	63	28			ENST00000369096.4:c.2284G>A	p.Val762Met	p.V762M	ENST00000369096	NM_001198.3	762	Gtg/Atg	0	0.478	AATTCTGGCCGTGGTCAGAAA
MICAL1	64780	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	109770958	109770958	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	159	17			ENST00000358807.3:c.1336A>G	p.Thr446Ala	p.T446A	ENST00000358807	NM_022765.3	446	Aca/Gca	0	0.607	TCTGGGGATGTCTGTGACAGA
FOXB2	442425	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	79635448	79635448	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61	17			ENST00000376708.1:c.878C>T	p.Ser293Phe	p.S293F	ENST00000376708	NM_001013735.1	293	tCc/tTc	0	0.662	CCCTTGGCGTCCGTCATGCAC
AKAP4	8852	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	49958837	49958837	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62	49			ENST00000358526.2:c.527G>A	p.Arg176His	p.R176H	ENST00000358526	NM_003886.2	176	cGt/cAt	0	0.443	CATTTCTAGACGTAGGTTTTG
DOPEY1	23033	broad.mit.edu;ucsc.edu	GRCh37	6	83839856	83839856	+	stop_gained	Nonsense_Mutation	SNP	C	C	T			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	56	23			ENST00000349129.2:c.2356C>T	p.Gln786Ter	p.Q786*	ENST00000349129	NM_015018.3	786	Cag/Tag	0	0.418	TGAGCATGTGCAGCCTCCACA
NOTCH1	4851	broad.mit.edu;ucsc.edu	GRCh37	9	139411837	139411837	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9	4			ENST00000277541.6:c.1442G>T	p.Gly481Val	p.G481V	ENST00000277541	NM_017617.3	481	gGc/gTc	0	0.647	ACCCTCGTAGCCTGTGGGGTG
SRPK2	6733	broad.mit.edu;ucsc.edu	GRCh37	7	104782648	104782648	+	synonymous_variant	Silent	SNP	T	T	C	rs56003957	byFrequency	TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	131	23			ENST00000393651.3:c.1350A>G	p.Pro450=	p.P450=	ENST00000393651	NM_182692.2	450	ccA/ccG	0	0.443	GTCGTCCATTTGGCAATTCAC
TRAPPC11	60684	broad.mit.edu;ucsc.edu	GRCh37	4	184628079	184628079	+	missense_variant	Missense_Mutation	SNP	T	T	G			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	72	8			ENST00000334690.6:c.3175T>G	p.Ser1059Ala	p.S1059A	ENST00000334690	NM_021942.5	1059	Tca/Gca	0	0.418	CTTCATGTTCTCAGGTCTCAA
LRRTM4	80059	broad.mit.edu;ucsc.edu	GRCh37	2	76975874	76975874	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	169	49			ENST00000409093.1:c.1720A>G	p.Thr574Ala	p.T574A	ENST00000409093		574	Acc/Gcc	0	0.617	CTGGCGATGGTGGCGATGAAG
ZW10	9183	broad.mit.edu;hgsc.bcm.edu	GRCh37	11	113614641	113614641	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	153	64			ENST00000200135.3:c.1394delA	p.Asn465IlefsTer19	p.N465Ifs*19	ENST00000200135	NM_004724.3	465	aAt/at	0	0.418	GTCCAATGTATTTTCAGGCTC
ATRX	546	broad.mit.edu;hgsc.bcm.edu	GRCh37	X	76874329	76874330	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T			TCGA-HT-7470-01	TCGA-HT-7470-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52	82			ENST00000373344.5:c.5392dupA	p.Arg1798LysfsTer12	p.R1798Kfs*12	ENST00000373344	NM_000489.3	1798	aga/aAga	0	0.322	TTTCATCACTCTGACATCTACC
INTS4	92105	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	77639508	77639508	+	synonymous_variant	Silent	SNP	A	A	T			TCGA-DH-5140-01	TCGA-DH-5140-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24	47			ENST00000534064.1:c.1251T>A	p.Val417=	p.V417=	ENST00000534064	NM_033547.3	417	gtT/gtA	0	0.443	TGAACATGTCAACTAGGAAAT
MAML2	84441	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	95712904	95712904	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-DH-5140-01	TCGA-DH-5140-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97	114			ENST00000524717.1:c.2679G>C	p.Gln893His	p.Q893H	ENST00000524717	NM_032427.1	893	caG/caC	0	0.408	TTGGGTTTCTCTGTTGGGTCA
ATN1	1822	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	7046127	7046127	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DH-5140-01	TCGA-DH-5140-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	216	17			ENST00000356654.4:c.1697C>T	p.Pro566Leu	p.P566L	ENST00000356654	NM_001007026.1	566	cCt/cTt	0	0.637	CCCAATGGCCCTCCAGTCTCT
SPTBN5	51332	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	42172441	42172441	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-DH-5140-01	TCGA-DH-5140-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18	8			ENST00000320955.6:c.2728T>C	p.Leu910=	p.L910=	ENST00000320955	NM_016642.3	910	Ttg/Ctg	0	0.632	TCCAGCCACAACTGGAGCTCC
ACAN	176	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	89398499	89398499	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DH-5140-01	TCGA-DH-5140-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58	40			ENST00000439576.2:c.2683C>T	p.Pro895Ser	p.P895S	ENST00000439576	NM_013227.3	895	Ccc/Tcc	0	0.572	AAGTGGACTGCCCTCTGGAGA
SLX4	84464	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	3640690	3640690	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DH-5140-01	TCGA-DH-5140-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	123	130			ENST00000294008.3:c.2949C>T	p.Tyr983=	p.Y983=	ENST00000294008	NM_032444.2	983	taC/taT	0	0.572	AGAGCTGTTCGTAATCCCCGG
ABCC12	94160	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	48174762	48174762	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DH-5140-01	TCGA-DH-5140-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	105	79			ENST00000311303.3:c.493C>T	p.Leu165=	p.L165=	ENST00000311303	NM_033226.2	165	Ctg/Ttg	0	0.537	GCTATGCACAGTCCAATGCCA
TP53	7157	hgsc.bcm.edu;broad.mit.edu	GRCh37	17	7574035	7574035	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G			TCGA-DH-5140-01	TCGA-DH-5140-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33	15			ENST00000269305.4:c.994-2A>C		p.X332_splice	ENST00000269305	NM_001126112.2			0	0.507	CCCACGGATCTGCAGCAACAG
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7577572	7577572	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-DH-5140-01	TCGA-DH-5140-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	77	45			ENST00000269305.4:c.709A>G	p.Met237Val	p.M237V	ENST00000269305	NM_001126112.2	237	Atg/Gtg	0	0.572	CTGTTACACATGTAGTTGTAG
NF1	4763	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	29556166	29556166	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-DH-5140-01	TCGA-DH-5140-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	12	101			ENST00000358273.4:c.2533T>C	p.Cys845Arg	p.C845R	ENST00000358273	NM_001042492.2	845	Tgt/Cgt	0	0.512	TGGCTTCCTTTGTGCCCTTGG
CCDC40	55036	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	78032380	78032380	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DH-5140-01	TCGA-DH-5140-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	12	120			ENST00000397545.4:c.1247G>A	p.Arg416His	p.R416H	ENST00000397545	NM_017950.3	416	cGc/cAc	0	0.537	GACGACATCCGCGTGATGACA
PLIN4	729359	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	4511095	4511095	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DH-5140-01	TCGA-DH-5140-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	83	34			ENST00000301286.3:c.2835C>T	p.Gly945=	p.G945=	ENST00000301286	NM_001080400.1	945	ggC/ggT	0	0.592	CATCCTTAGCGCCACTCAGCA
NOTCH3	4854	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	15281250	15281250	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DH-5140-01	TCGA-DH-5140-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	65	45			ENST00000263388.2:c.5006G>A	p.Arg1669His	p.R1669H	ENST00000263388	NM_000435.2	1669	cGc/cAc	0	0.677	GCTGTGCTCGCGCTTGCGCCG
SLC7A9	11136	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	33350866	33350866	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-DH-5140-01	TCGA-DH-5140-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	80	21			ENST00000023064.4:c.754C>A	p.Leu252Met	p.L252M	ENST00000023064	NM_014270.4	252	Ctg/Atg	0	0.602	GCCAAAGGCAGGTTTCTGGGA
LPHN2	23266	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	82456736	82456736	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-DH-5140-01	TCGA-DH-5140-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69	48			ENST00000319517.6:c.4119T>C	p.Asn1373=	p.N1373=	ENST00000319517	NM_012302.2	1373	aaT/aaC	0	0.428	gcaggggcaatagtgatggtt
RFWD2	64326	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	176132075	176132075	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-DH-5140-01	TCGA-DH-5140-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99	85			ENST00000367669.3:c.692A>G	p.Asp231Gly	p.D231G	ENST00000367669	NM_022457.5	231	gAt/gGt	0	0.358	ATCAAGGTTATCTTGGTCAGT
RBM11	54033	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	21	15599378	15599378	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DH-5140-01	TCGA-DH-5140-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	373	100			ENST00000400577.3:c.610G>A	p.Ala204Thr	p.A204T	ENST00000400577	NM_144770.3	204	Gct/Act	0	0.463	TCAGATGACAGCTCCACTTCC
APOB	338	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	21228172	21228172	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DH-5140-01	TCGA-DH-5140-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	131	110			ENST00000233242.1:c.11568C>T	p.Ile3856=	p.I3856=	ENST00000233242	NM_000384.2	3856	atC/atT	0	0.473	GCTCAGGCACGATGATGGTGG
ACOXL	55289	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	111562956	111562956	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DH-5140-01	TCGA-DH-5140-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	121	76			ENST00000439055.1:c.737C>T	p.Ala246Val	p.A246V	ENST00000439055	NM_001142807.1	246	gCt/gTt	0	0.453	GCTTTCCAAGCTATGGGTGCC
NDUFAF3	25915	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	49059582	49059582	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-DH-5140-01	TCGA-DH-5140-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	22	13			ENST00000326925.6:c.5C>G	p.Ala2Gly	p.A2G	ENST00000326925	NM_199069.1	2	gCc/gGc	0	0.716	TCAGCCATGGCCACCGCTCTC
UBXN7	26043	hgsc.bcm.edu;broad.mit.edu	GRCh37	3	196094958	196094958	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DH-5140-01	TCGA-DH-5140-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	243	20			ENST00000296328.4:c.775G>A	p.Gly259Ser	p.G259S	ENST00000296328	NM_015562.1	259	Ggt/Agt	0	0.398	CCATGTTCACCCAGAAATCCC
HIST1H4G	8369	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	26247163	26247163	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DH-5140-01	TCGA-DH-5140-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	105	20			ENST00000244537.4:c.43G>A	p.Gly15Ser	p.G15S	ENST00000244537	NM_003547.2	15	Ggt/Agt	0	0.517	CACTTGGCACCGCCTTTCCCA
HLA-DQA2	3118	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	32713607	32713607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144060347		TCGA-DH-5140-01	TCGA-DH-5140-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	127	130			ENST00000374940.3:c.371C>T	p.Thr124Met	p.T124M	ENST00000374940	NM_020056.4	124	aCg/aTg	0	0.507	TTTCCTGTGACGCTGGGTCAG
SLC25A40	55972	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	87466058	87466058	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DH-5140-01	TCGA-DH-5140-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	72	28			ENST00000341119.5:c.891C>T	p.Ser297=	p.S297=	ENST00000341119	NM_018843.3	297	tcC/tcT	0	0.259	AAAATAATCCGGAAAATCCAT
CPA1	1357	hgsc.bcm.edu;broad.mit.edu	GRCh37	7	130024455	130024455	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DH-5140-01	TCGA-DH-5140-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	151	12			ENST00000011292.3:c.775G>A	p.Ala259Thr	p.A259T	ENST00000011292	NM_001868.2	259	Gct/Act	0	0.602	GAACTGGGACGCTGGCTTTGG
ZCRB1	85437	broad.mit.edu;ucsc.edu	GRCh37	12	42711595	42711595	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-DH-5140-01	TCGA-DH-5140-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	137	90			ENST00000266529.3:c.219C>A	p.Asn73Lys	p.N73K	ENST00000266529	NM_033114.3	73	aaC/aaA	0	0.393	TTACCTGTTTGTTGTTTATTG
UGGT1	56886	broad.mit.edu;hgsc.bcm.edu	GRCh37	2	128938471	128938471	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-			TCGA-DH-5140-01	TCGA-DH-5140-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73	54			ENST00000259253.6:c.3908delT	p.Ile1303AsnfsTer47	p.I1303Nfs*47	ENST00000259253	NM_020120.3	1303	aTa/aa	0	0.373	TAGGAGTTTATACCTTACATG
TP63	8626	broad.mit.edu;hgsc.bcm.edu	GRCh37	3	189612149	189612149	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-			TCGA-DH-5140-01	TCGA-DH-5140-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	155	107			ENST00000264731.3:c.1904delG	p.Gly635ValfsTer69	p.G635Vfs*69	ENST00000264731	NM_003722.4	634	cGg/cg	0	0.567	AGTGAGACCCGGGGTGAGCGT
TP53	7157	broad.mit.edu;hgsc.bcm.edu	GRCh37	17	7574025	7574025	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-			TCGA-DH-5140-01	TCGA-DH-5140-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	38	19			ENST00000269305.4:c.1002delG	p.Arg335ValfsTer10	p.R335Vfs*10	ENST00000269305	NM_001126112.2	334	ggG/gg	0	0.522	AGCGCTCACGCCCACGGATCT
CCKBR	887	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	6292257	6292257	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	117	14			ENST00000334619.2:c.828C>T	p.Asn276=	p.N276=	ENST00000334619	NM_176875.3	276	aaC/aaT	0	0.662	TTCACCAGAACGGGCGTTGCC
MADD	8567	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	47304014	47304014	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95	10			ENST00000311027.5:c.1552C>T	p.Arg518Trp	p.R518W	ENST00000311027	NM_003682.3	518	Cgg/Tgg	0	0.562	CCTCTTTCCTCGGCCTGTGGT
OR5L1	219437	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	55579059	55579059	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	225	33			ENST00000333973.2:c.117G>T	p.Leu39Phe	p.L39F	ENST00000333973	NM_001004738.1	39	ttG/ttT	0	0.507	GAGTCACGTTGTTAGCCAACC
DYNC2H1	79659	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	102995846	102995846	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	16	8			ENST00000398093.3:c.1679G>A	p.Arg560Gln	p.R560Q	ENST00000398093		560	cGa/cAa	0	0.333	GCTAGTAGTCGAATTATGGAA
BRF1	2972	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	14	105688184	105688184	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23	4			ENST00000546474.1:c.1116C>T	p.Ala372=	p.A372=	ENST00000546474	NM_001519.3	372	gcC/gcT	0	0.637	GGCTGGCCGCGGCTTCCAGCT
NPAP1	23742	hgsc.bcm.edu;broad.mit.edu	GRCh37	15	24921093	24921093	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	20	6			ENST00000329468.2:c.79C>A	p.Pro27Thr	p.P27T	ENST00000329468	NM_018958.2	27	Ccc/Acc	0	0.701	CGCCCCCGCTCCCCTGTCCCG
ATP10A	57194	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	25959052	25959052	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91	22			ENST00000356865.6:c.2113T>C	p.Tyr705His	p.Y705H	ENST00000356865	NM_024490.3	705	Tat/Cat	0	0.662	CTGGCCGCATACACCAGTGCG
HS3ST6	64711	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	1962006	1962006	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42	9			ENST00000443547.1:c.521G>A	p.Arg174His	p.R174H	ENST00000443547	NM_001009606.2	174	cGc/cAc	0	0.716	GGCCAGGGCGCGGAAGCTGGG
LPO	4025	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	56343663	56343663	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	63	8			ENST00000262290.4:c.1669C>T	p.Arg557Cys	p.R557C	ENST00000262290	NM_006151.2	557	Cgt/Tgt	0	0.502	CAACACACAGCGTTGCCGGGA
MAP1S	55201	hgsc.bcm.edu;broad.mit.edu	GRCh37	19	17845112	17845112	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs71762031		TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64	6			ENST00000324096.4:c.3055G>C	p.Ala1019Pro	p.A1019P	ENST00000324096	NM_018174.4	1019	Gcc/Ccc	0	0.657	CGACTCGGTGGCCATGCATAC
ZNF536	9745	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	31040081	31040081	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	72	9			ENST00000355537.3:c.3555C>T	p.Thr1185=	p.T1185=	ENST00000355537	NM_014717.1	1185	acC/acT	0	0.572	ATGTTGAAACCGAACCGGAAA
LILRB2	10288	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	54783825	54783825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141797988		TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	182	24			ENST00000391749.4:c.176G>A	p.Arg59His	p.R59H	ENST00000391749	NM_001278406.1	59	cGt/cAt	0	0.547	CCTATATAGACGGTACTCCTG
LILRA3	11026	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	54803127	54803127	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	182	23			ENST00000251390.3:c.550G>A	p.Val184Met	p.V184M	ENST00000251390	NM_006865.3	184	Gtg/Atg	0	0.567	ACGGGGCCCACGGAGAAGATG
TAS1R2	80834	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	19181133	19181133	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47	6			ENST00000375371.3:c.831C>T	p.Pro277=	p.P277=	ENST00000375371	NM_152232.2	277	ccC/ccT	0	0.632	GGGTCAGGTCGGGCGAGAACA
GLIS1	148979	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	53995560	53995560	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68	11			ENST00000312233.2:c.861G>A	p.Thr287=	p.T287=	ENST00000312233	NM_147193.2	287	acG/acA	0	0.637	GCTTCTCGCCCGTGTGGCTCC
SRSF11	9295	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	70715634	70715634	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41	5			ENST00000370950.3:c.1023-1G>C		p.X341_splice	ENST00000370950				0	0.418	TGTGATTCTAGAGAGAGACGA
FMO3	2328	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	171079965	171079965	+	synonymous_variant	Silent	SNP	C	C	G			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	107	11			ENST00000367755.4:c.654C>G	p.Ser218=	p.S218=	ENST00000367755	NM_001002294.2	218	tcC/tcG	0	0.473	GAAGTGGCTCCTGGGTGATGA
CFH	3075	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	196716352	196716352	+	missense_variant	Missense_Mutation	SNP	A	A	T			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	89	17			ENST00000367429.4:c.3605A>T	p.Lys1202Ile	p.K1202I	ENST00000367429	NM_000186.3	1202	aAa/aTa	0	0.383	TTTGTGTGTAAACGGGGATAT
KDM5B	10765	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	202702739	202702739	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73	16			ENST00000367265.3:c.3699G>A	p.Leu1233=	p.L1233=	ENST00000367265	NM_006618.3	1233	ctG/ctA	0	0.532	CGAGCAGGGGCAGAATTTTCT
OBSCN	84033	hgsc.bcm.edu;ucsc.edu	GRCh37	1	228487678	228487678	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	59	10			ENST00000570156.2:c.13570G>A	p.Val4524Met	p.V4524M	ENST00000570156	NM_001271223.2	4524	Gtg/Atg	0	0.557	GGCGGCCCCCGTGGAGTGGAG
OR13G1	441933	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	247835492	247835492	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93	17			ENST00000359688.2:c.852G>A	p.Pro284=	p.P284=	ENST00000359688	NM_001005487.1	284	ccG/ccA	0	0.438	TGTACACCATCGGGTTTAATG
XKR7	343702	hgsc.bcm.edu;broad.mit.edu	GRCh37	20	30584347	30584347	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36	7			ENST00000562532.2:c.827C>T	p.Thr276Met	p.T276M	ENST00000562532	NM_001011718.1	276	aCg/aTg	0	0.701	CTGGCCTGGACGCTGGCCTCC
DPP10	57628	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	116497433	116497433	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	134	22			ENST00000393147.2:c.828G>A	p.Ala276=	p.A276=	ENST00000393147	NM_001178034.1	276	gcG/gcA	0	0.458	TTACTGGAGCGTTGTATCCCA
CWC22	57703	hgsc.bcm.edu;broad.mit.edu	GRCh37	2	180810177	180810177	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	126	9			ENST00000410053.3:c.2406T>C	p.Asn802=	p.N802=	ENST00000410053	NM_020943.2	802	aaT/aaC	0	0.353	GGTCTCTGTCATTCGCAACTC
CEP97	79598	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	101476897	101476897	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	81	17			ENST00000341893.3:c.1447C>T	p.Pro483Ser	p.P483S	ENST00000341893		483	Cct/Tct	0	0.378	TGGACTATTACCTTGTCCTGA
PIK3CA	5290	hgsc.bcm.edu;broad.mit.edu	GRCh37	3	178922364	178922364	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52	4			ENST00000263967.3:c.1133G>A	p.Cys378Tyr	p.C378Y	ENST00000263967	NM_006218.2	378	tGt/tAt	0	0.328	AGAGTACCTTGTTCCAATCCC
B3GNT5	84002	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	182988131	182988131	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82	19			ENST00000326505.3:c.545A>G	p.Tyr182Cys	p.Y182C	ENST00000326505	NM_032047.4	182	tAt/tGt	0	0.333	GCAAATACCTATTGTCCACAT
PDGFRA	5156	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	55131161	55131161	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	136	551			ENST00000257290.5:c.704G>A	p.Cys235Tyr	p.C235Y	ENST00000257290	NM_006206.4	235	tGt/tAt	0	0.443	GTGGTCACCTGTGCTGTTTTT
TET2	54790	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	106157894	106157894	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	43	12			ENST00000380013.4:c.2795A>G	p.Asp932Gly	p.D932G	ENST00000380013	NM_001127208.2	932	gAc/gGc	0	0.453	CCTGTGCCTGACCAGGGAGGA
SLC6A3	6531	hgsc.bcm.edu;broad.mit.edu	GRCh37	5	1406358	1406358	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	131	10			ENST00000270349.9:c.1544G>A	p.Arg515Gln	p.R515Q	ENST00000270349	NM_001044.4	515	cGg/cAg	0	0.652	CAGGCTGGGCCGCTGCCCGGT
SLC6A3	6531	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	1406386	1406386	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	132	14			ENST00000270349.9:c.1516G>A	p.Asp506Asn	p.D506N	ENST00000270349	NM_001044.4	506	Gac/Aac	0	0.642	TGGATGTCGTCGCTGAACTGC
SLCO4C1	353189	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	101582955	101582955	+	splice_donor_variant	Splice_Site	SNP	C	C	A			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	50	9			ENST00000310954.6:c.1811+1G>T		p.X604_splice	ENST00000310954	NM_180991.4			0	0.378	GTGCTACATACCTTAGGATAG
PRSS35	167681	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	84233953	84233953	+	stop_gained	Nonsense_Mutation	SNP	C	C	T			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64	8			ENST00000536636.1:c.793C>T	p.Arg265Ter	p.R265*	ENST00000536636	NM_001170423.1	265	Cga/Tga	0	0.527	GGGCTGGGCACGAGGAGGCAT
SAMD3	154075	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	130497110	130497110	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45	10			ENST00000368134.2:c.698G>A	p.Arg233Gln	p.R233Q	ENST00000368134	NM_001258275.1	233	cGa/cAa	0	0.343	TATGGGTCTTCGAACATATTT
PDE7B	27115	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	136494954	136494954	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45	12			ENST00000308191.6:c.731A>G	p.Asn244Ser	p.N244S	ENST00000308191	NM_018945.3	244	aAt/aGt	0	0.428	GTGCTGGAGAATCATCACTGG
PPP1R3A	5506	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	113517983	113517983	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	162	18			ENST00000284601.3:c.3164C>T	p.Pro1055Leu	p.P1055L	ENST00000284601	NM_002711.3	1055	cCt/cTt	0	0.363	TTCCTCAACAGGAAGACTAGT
ASZ1	136991	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	117067417	117067417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113501399		TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	164	25			ENST00000284629.2:c.98C>T	p.Thr33Met	p.T33M	ENST00000284629	NM_130768.2	33	aCg/aTg	0	0.657	TACCTGAGACGTCCGGTCGAG
KDM7A	80853	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	139810958	139810958	+	missense_variant	Missense_Mutation	SNP	A	A	C			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	38	7			ENST00000397560.2:c.1365T>G	p.Ile455Met	p.I455M	ENST00000397560	NM_030647.1	455	atT/atG	0	0.294	CATTGTCTGGAATTTCAAAGG
TAS2R40	259286	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	142919425	142919425	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	119	12			ENST00000408947.3:c.254G>A	p.Arg85Gln	p.R85Q	ENST00000408947	NM_176882.1	85	cGa/cAa	0	0.433	CTGCTATTCCGAATTGTTTAT
EFCAB1	79645	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	49643961	49643961	+	stop_gained	Nonsense_Mutation	SNP	G	G	A			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	32	6			ENST00000262103.3:c.160C>T	p.Arg54Ter	p.R54*	ENST00000262103	NM_024593.3	54	Cga/Tga	0	0.393	AGGATGTTTCGAAATGCATTA
ASS1	445	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	133333962	133333962	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24	5			ENST00000372394.1:c.349G>A	p.Gly117Ser	p.G117S	ENST00000372394		117	Ggc/Agc	0	0.657	TGTGTCCCACGGCGCCACAGG
AKAP4	8852	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	49958224	49958224	+	synonymous_variant	Silent	SNP	G	G	A	rs140947270		TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	20	7			ENST00000358526.2:c.1140C>T	p.Ser380=	p.S380=	ENST00000358526	NM_003886.2	380	tcC/tcT	0	0.463	CAATCAAATCGGACACAATCT
C6orf10	10665	broad.mit.edu;ucsc.edu	GRCh37	6	32261388	32261388	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	126	21			ENST00000447241.2:c.1062G>A	p.Thr354=	p.T354=	ENST00000447241	NM_006781.3	354	acG/acA	0	0.468	ACCCACTCTTCGTTACTTGGG
TEAD3	7005	broad.mit.edu;ucsc.edu	GRCh37	6	35445110	35445110	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23	3			ENST00000338863.7:c.570G>A	p.Pro190=	p.P190=	ENST00000338863	NM_003214.3	190	ccG/ccA	0	0.627	GCGGCAGGGGCGGCTGGATGG
HCK	3055	broad.mit.edu;ucsc.edu	GRCh37	20	30667667	30667667	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	25	4			ENST00000375852.2:c.519C>T	p.Ser173=	p.S173=	ENST00000375852		173	agC/agT	0	0.612	TCCGGGATAGCGAGACCACTA
IGHV3-53	28420	broad.mit.edu;ucsc.edu	GRCh37	14	107048694	107048694	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	241	33			ENST00000390627.2:c.326C>T	p.Thr109Met	p.T109M	ENST00000390627		109	aCg/aTg	0	0.552	ATACACGGCCGTGTCCTCGGC
SURF2	6835	broad.mit.edu;ucsc.edu	GRCh37	9	136227174	136227174	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52	4			ENST00000371964.4:c.551C>T	p.Thr184Met	p.T184M	ENST00000371964	NM_001278928.1	184	aCg/aTg	0	0.527	CTTGGAAGCACGGAGGATGGG
CDC20B	166979	broad.mit.edu;ucsc.edu	GRCh37	5	54424345	54424345	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69	8			ENST00000381375.2:c.798C>A	p.Asn266Lys	p.N266K	ENST00000381375		266	aaC/aaA	0	0.448	TTAAGTCTATGTTTTCAATCC
MKI67	4288	broad.mit.edu;ucsc.edu	GRCh37	10	129902797	129902797	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	103	25			ENST00000368654.3:c.7307A>G	p.Asp2436Gly	p.D2436G	ENST00000368654	NM_002417.4	2436	gAc/gGc	0	0.473	GCCAACCAGGTCCTCTAGAGC
PCDH11X	27328	broad.mit.edu;ucsc.edu	GRCh37	X	91133911	91133911	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-HT-7882-01	TCGA-HT-7882-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	44	15			ENST00000373094.1:c.2672C>A	p.Thr891Asn	p.T891N	ENST00000373094	NM_032968.3	891	aCt/aAt	0	0.373	ATTGAAGAAACTAAGGCAGAT
TTC17	55761	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	43423074	43423074	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HW-A5KL-01	TCGA-HW-A5KL-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24	11			ENST00000039989.4:c.1298G>A	p.Arg433His	p.R433H	ENST00000039989	NM_018259.5	433	cGt/cAt	0	0.373	CGCTATCATCGTGGAGATATC
FANCM	57697	hgsc.bcm.edu;ucsc.edu	GRCh37	14	45645153	45645153	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-HW-A5KL-01	TCGA-HW-A5KL-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35	4			ENST00000267430.5:c.3196C>G	p.Leu1066Val	p.L1066V	ENST00000267430	NM_020937.2	1066	Ctt/Gtt	0	0.303	AAAAAGTTGCCTTTATGATAT
CRAMP1L	57585	hgsc.bcm.edu;broad.mit.edu	GRCh37	16	1718033	1718033	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HW-A5KL-01	TCGA-HW-A5KL-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	43	22			ENST00000397412.3:c.3173C>T	p.Ser1058Phe	p.S1058F	ENST00000397412		1058	tCc/tTc	0	0.602	ATACCGCTGTCCTCGTCAGAG
XYLT1	64131	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	17202869	17202869	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HW-A5KL-01	TCGA-HW-A5KL-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40	50			ENST00000261381.6:c.2563G>A	p.Ala855Thr	p.A855T	ENST00000261381	NM_022166.3	855	Gca/Aca	0	0.562	AGCTTCAGTGCCTCCTCTGAA
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7577586	7577586	+	missense_variant	Missense_Mutation	SNP	A	A	C			TCGA-HW-A5KL-01	TCGA-HW-A5KL-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10	41			ENST00000269305.4:c.695T>G	p.Ile232Ser	p.I232S	ENST00000269305	NM_001126112.2	232	aTc/aGc	0	0.552	GTTGTAGTGGATGGTGGTACA
PLVAP	83483	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	17476154	17476154	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-HW-A5KL-01	TCGA-HW-A5KL-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	72	44			ENST00000252590.4:c.1120C>G	p.Gln374Glu	p.Q374E	ENST00000252590	NM_031310.1	374	Cag/Gag	0	0.622	ATCCTGAGCTGCTCCGCCTCC
CYP2B6	1555	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	41515236	41515236	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HW-A5KL-01	TCGA-HW-A5KL-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	147	72			ENST00000324071.4:c.758G>A	p.Arg253His	p.R253H	ENST00000324071	NM_000767.4	253	cGt/cAt	0	0.527	GAGAAGCACCGTGAAACCCTG
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HW-A5KL-01	TCGA-HW-A5KL-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	43	19			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
EFHC2	80258	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	44120532	44120532	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HW-A5KL-01	TCGA-HW-A5KL-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35	23			ENST00000420999.1:c.395G>A	p.Arg132Gln	p.R132Q	ENST00000420999	NM_025184.3	132	cGg/cAg	0	0.413	CCGATGACGCCGGATAGAAGT
ALAS2	212	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	55052378	55052378	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HW-A5KL-01	TCGA-HW-A5KL-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64	15			ENST00000330807.5:c.56C>T	p.Thr19Ile	p.T19I	ENST00000330807	NM_000032.4	19	aCa/aTa	0	0.542	TAGGAGGCTTGTGGGGCCCCG
UBQLN2	29978	hgsc.bcm.edu;ucsc.edu	GRCh37	X	56590705	56590705	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HW-A5KL-01	TCGA-HW-A5KL-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	55	8			ENST00000338222.5:c.399C>T	p.Ser133=	p.S133=	ENST00000338222	NM_013444.3	133	tcC/tcT	0	0.572	GGAGTAACTCCACACCTATTT
ATRX	546	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	76939961	76939961	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HW-A5KL-01	TCGA-HW-A5KL-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	109	117			ENST00000373344.5:c.787T>C	p.Trp263Arg	p.W263R	ENST00000373344	NM_000489.3	263	Tgg/Cgg	0	0.393	TAGCAATACCATTGGTTGTTT
DCAF12L2	340578	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	125299672	125299672	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HW-A5KL-01	TCGA-HW-A5KL-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57	28			ENST00000538699.1:c.236C>T	p.Ala79Val	p.A79V	ENST00000538699	NM_001013628.2	79	gCc/gTc	0	0.706	CCTCTGGACGGCGTAGCCCCG
PLXNB3	5365	broad.mit.edu;ucsc.edu	GRCh37	X	153039467	153039467	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-HW-A5KL-01	TCGA-HW-A5KL-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	66	28			ENST00000538966.1:c.3502C>A	p.Gln1168Lys	p.Q1168K	ENST00000538966	NM_001163257.1	1168	Cag/Aag	0	0.672	CTTCCTGTACCAGCCCAACCC
OR1D2	4991	broad.mit.edu;ucsc.edu	GRCh37	17	2995927	2995927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs73300984	byFrequency	TCGA-HW-A5KL-01	TCGA-HW-A5KL-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	105	21			ENST00000331459.1:c.364C>T	p.Arg122Cys	p.R122C	ENST00000331459	NM_002548.2	122	Cgc/Tgc	0	0.537	GCCACATAGCGGTCATATGCC
IPO8	10526	broad.mit.edu;ucsc.edu	GRCh37	12	30827606	30827606	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HW-A5KL-01	TCGA-HW-A5KL-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	128	76			ENST00000256079.4:c.811C>T	p.Arg271Trp	p.R271W	ENST00000256079	NM_006390.3	271	Cgg/Tgg	0	0.418	TCAAAGAGCCGAGCTACAATA
GRIP2	80852	broad.mit.edu;ucsc.edu	GRCh37	3	14535207	14535207	+	non_coding_transcript_exon_variant	RNA	SNP	C	C	T			TCGA-HW-A5KL-01	TCGA-HW-A5KL-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9	10			ENST00000273083.3:n.3163G>A		*1055*	ENST00000273083				0	0.672	GCCTGGCGATCGGGGGGCCCG
RLIM	51132	broad.mit.edu;hgsc.bcm.edu	GRCh37	X	73812199	73812200	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs61752449		TCGA-HW-A5KL-01	TCGA-HW-A5KL-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33	30			ENST00000332687.6:c.950dupC	p.Thr318AsnfsTer5	p.T318Nfs*5	ENST00000332687	NM_016120.3	317	cca/ccCa	0	0.48	GGACTATGGTTGGAGGTCTCTG
GATA3	2625	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	8100386	8100386	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	166	101			ENST00000346208.3:c.360G>A	p.Thr120=	p.T120=	ENST00000346208		120	acG/acA	0	0.697	TCTCCAAGACGTCCATCCACC
FRMD4A	55691	hgsc.bcm.edu;broad.mit.edu	GRCh37	10	13698931	13698931	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8	4			ENST00000357447.2:c.2658C>T	p.Gly886=	p.G886=	ENST00000357447	NM_018027.3	886	ggC/ggT	0	0.716	CGTCGCCGCCGCCGCCGCGCC
OR4X2	119764	hgsc.bcm.edu;broad.mit.edu	GRCh37	11	48267032	48267032	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99	6			ENST00000302329.3:c.377C>G	p.Thr126Ser	p.T126S	ENST00000302329	NM_001004727.1	126	aCc/aGc	0	0.498	AGCTACACCACCATCATGAAC
CPSF7	79869	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	61178544	61178544	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	86	58			ENST00000340437.4:c.1416C>T	p.Ser472=	p.S472=	ENST00000340437	NM_024811.3	472	agC/agT	0	0.502	CCCGGGACCGGCTAGGTGACC
TYR	7299	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	88961080	88961080	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs61754389		TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	131	23			ENST00000263321.5:c.1126C>G	p.Gln376Glu	p.Q376E	ENST00000263321	NM_000372.4	376	Cag/Gag	0	0.413	AACAATGTCCCAGGTACAGGG
C11orf65	160140	hgsc.bcm.edu;broad.mit.edu	GRCh37	11	108256655	108256655	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	236	14			ENST00000393084.1:c.779A>G	p.Asn260Ser	p.N260S	ENST00000393084	NM_152587.3	260	aAc/aGc	0	0.333	ACCTTTGAAGTTAGCCGAAGA
NNMT	4837	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	114182852	114182852	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90	96			ENST00000535401.1:c.448G>A	p.Gly150Arg	p.G150R	ENST00000535401		150	Ggg/Agg	0	0.602	CCAGCCACTGGGGGCCGTCCC
ITPR2	3709	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	26985668	26985668	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	165	33			ENST00000381340.3:c.47C>T	p.Ser16Phe	p.S16F	ENST00000381340	NM_002223.2	16	tCc/tTc	0	0.622	CGCGTACAGGGACACGATGTC
IGDCC4	57722	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	65684524	65684524	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95	59			ENST00000352385.2:c.2070G>A	p.Val690=	p.V690=	ENST00000352385	NM_020962.1	690	gtG/gtA	0	0.622	GGACAGGCCCCACATCCCAAG
MGRN1	23295	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	4732911	4732911	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	20	14			ENST00000262370.7:c.1446C>T	p.Gly482=	p.G482=	ENST00000262370	NM_015246.3	482	ggC/ggT	0	0.701	CACTGGGTGGCGCAGAGCTGG
IRF8	3394	hgsc.bcm.edu;broad.mit.edu	GRCh37	16	85952180	85952180	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6	16			ENST00000268638.5:c.759G>A	p.Pro253=	p.P253=	ENST00000268638	NM_002163.2	253	ccG/ccA	0	0.741	TGCGCTTCCCGCCGGCCGACG
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	72	51			ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	0	0.567	AACTGTTACACATGTAGTTGT
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	50	24			ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	0	0.552	CCTTCCACTCGGATAAGATGC
CLUL1	27098	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	18	618009	618009	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40	8			ENST00000400606.2:c.9G>A	p.Pro3=	p.P3=	ENST00000400606	NM_014410.4	3	ccG/ccA	0	0.448	ACATGAAGCCGCCACTCTTGG
LIPG	9388	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	18	47107968	47107968	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91	69			ENST00000261292.4:c.977T>C	p.Met326Thr	p.M326T	ENST00000261292	NM_006033.2	326	aTg/aCg	0	0.493	GCCAAGAAAATGAGGAACAAG
NFATC1	4772	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	18	77227575	77227575	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61	28			ENST00000329101.4:c.2046C>T	p.Pro682=	p.P682=	ENST00000329101	NM_172387.2	682	ccC/ccT	0	0.532	CCTACCTTCCCGCCAACGGTA
MUC16	94025	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	9062722	9062722	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	32	33			ENST00000397910.4:c.24724A>G	p.Thr8242Ala	p.T8242A	ENST00000397910	NM_024690.2	8242	Acc/Gcc	0	0.498	ACAAGAGTGGTCATCTCTGAG
HKR1	284459	hgsc.bcm.edu;broad.mit.edu	GRCh37	19	37838730	37838730	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	63	4			ENST00000324411.4:c.269C>T	p.Ala90Val	p.A90V	ENST00000324411	NM_181786.2	90	gCg/gTg	0	0.493	CGAGGGGAAGCGCCCTGGAGA
RYR1	6261	hgsc.bcm.edu;broad.mit.edu	GRCh37	19	38995497	38995497	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	59	4			ENST00000359596.3:c.8177A>G	p.Lys2726Arg	p.K2726R	ENST00000359596		2726	aAg/aGg	0	0.597	GCAGAGAAAAAGGCCACAGTG
ZC3H4	23211	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	47593321	47593321	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84	45			ENST00000253048.5:c.618C>T	p.Gly206=	p.G206=	ENST00000253048	NM_015168.1	206	ggC/ggT	0	0.577	CCTCCTCGTCGCCCTCATATT
FASLG	356	hgsc.bcm.edu;broad.mit.edu	GRCh37	1	172634805	172634805	+	synonymous_variant	Silent	SNP	C	C	A	rs80358236		TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	81	5			ENST00000367721.2:c.495C>A	p.Thr165=	p.T165=	ENST00000367721	NM_000639.1	165	acC/acA	0	0.428	GGGAAGACACCTATGGAATTG
C20orf194	25943	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	20	3356865	3356865	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	31	50			ENST00000252032.9:c.368A>G	p.His123Arg	p.H123R	ENST00000252032	NM_001009984.2	123	cAt/cGt	0	0.368	ATTTCTCCAATGTGCCACATA
PCK1	5105	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	20	56139236	56139236	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47	12			ENST00000319441.4:c.973G>A	p.Ala325Thr	p.A325T	ENST00000319441	NM_002591.3	325	Gcc/Acc	0	0.448	TCATTTAAGGGCCATCAACCC
APOB	338	hgsc.bcm.edu;broad.mit.edu	GRCh37	2	21230555	21230555	+	stop_gained	Nonsense_Mutation	SNP	A	A	C			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	72	6			ENST00000233242.1:c.9185T>G	p.Leu3062Ter	p.L3062*	ENST00000233242	NM_000384.2	3062	tTa/tGa	0	0.408	TGTTAACCTTAATGGAAAACG
TEKT4	150483	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	95542422	95542422	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45	23			ENST00000295201.4:c.1216G>A	p.Ala406Thr	p.A406T	ENST00000295201	NM_144705.2	406	Gcc/Acc	0	0.592	GGACATTGCCGCCATGACCAA
ZEB2	9839	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	145147369	145147369	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	66	27			ENST00000558170.2:c.3294A>G	p.Lys1098=	p.K1098=	ENST00000558170	NM_014795.3	1098	aaA/aaG	0	0.617	CCAAGTGCCCTTTCTCGCGCG
LRP2	4036	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	170030513	170030513	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	54	37			ENST00000263816.3:c.10930A>G	p.Asn3644Asp	p.N3644D	ENST00000263816	NM_004525.2	3644	Aat/Gat	0	0.542	CAGCGGCCATTAGCACACCGA
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913499		TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	56	67			ENST00000345146.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000345146	NM_005896.2	132	Cgt/Agt	0	0.398	TAAGCATGACGACCTATGATG
ZFAND2B	130617	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	220072487	220072487	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97	12			ENST00000289528.5:c.268C>G	p.Gln90Glu	p.Q90E	ENST00000289528	NM_001270999.1	90	Cag/Gag	0	0.557	TGATCCAGCACAGCAAAAACG
OR5H1	26341	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	97852349	97852349	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	43	41			ENST00000354565.2:c.808C>G	p.Gln270Glu	p.Q270E	ENST00000354565	NM_001005338.1	270	Caa/Gaa	0	0.428	AGCAGATGATCAAGATATGGT
ACAD9	28976	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	128628194	128628194	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	113	57			ENST00000308982.7:c.1493C>G	p.Ala498Gly	p.A498G	ENST00000308982	NM_014049.4	498	gCc/gGc	0	0.587	TAGGACAGTGCCAACAAGTTT
AADACL2	344752	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	151461908	151461908	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79	55			ENST00000356517.3:c.389G>C	p.Arg130Thr	p.R130T	ENST00000356517	NM_207365.3	130	aGa/aCa	0	0.358	TTCCTGAATAGATGGACGGCA
GPBP1	65056	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	56546841	56546841	+	stop_gained	Nonsense_Mutation	SNP	C	C	T			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	32	18			ENST00000264779.6:c.1054C>T	p.Arg352Ter	p.R352*	ENST00000264779	NM_001127236.2	352	Cga/Tga	0	0.353	GGATATAAACCGAAACTTCGA
KIF6	221458	hgsc.bcm.edu;broad.mit.edu	GRCh37	6	39513460	39513460	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	65	4			ENST00000287152.7:c.1186G>C	p.Glu396Gln	p.E396Q	ENST00000287152	NM_145027.4	396	Gaa/Caa	0	0.338	ATTAGTTTTTCCAGCCTAAAA
C6orf118	168090	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	165715396	165715396	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	135	21			ENST00000230301.8:c.415T>C	p.Ser139Pro	p.S139P	ENST00000230301	NM_144980.3	139	Tcc/Ccc	0	0.627	GAAGTGTGGGAAAGAGAGGCC
SDK1	221935	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	4185446	4185446	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	56	97			ENST00000404826.2:c.4321G>A	p.Asp1441Asn	p.D1441N	ENST00000404826	NM_152744.3	1441	Gac/Aac	0	0.667	CACAGCCACCGACCTGGCCCC
PKD1L1	168507	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	47897211	47897211	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	19	14			ENST00000289672.2:c.4582C>T	p.Pro1528Ser	p.P1528S	ENST00000289672	NM_138295.3	1528	Cct/Tct	0	0.493	ACCTGCCCAGGAGCTTGGCTC
PCLO	27445	hgsc.bcm.edu;broad.mit.edu	GRCh37	7	82580131	82580131	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	153	11			ENST00000333891.9:c.9773A>G	p.Glu3258Gly	p.E3258G	ENST00000333891	NM_033026.5	3258	gAg/gGg	0	0.453	CTGCAGCTCCTCCAACTTTTT
ABCB1	5243	hgsc.bcm.edu;broad.mit.edu	GRCh37	7	87214993	87214993	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41	19			ENST00000265724.3:c.121C>T	p.Arg41Cys	p.R41C	ENST00000265724	NM_000927.4	41	Cgc/Tgc	0	0.378	TTTGAATAGCGAAACTAAAAA
DOCK4	9732	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	111617325	111617325	+	missense_variant	Missense_Mutation	SNP	T	T	A			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8	11			ENST00000437633.1:c.563A>T	p.His188Leu	p.H188L	ENST00000437633	NM_014705.3	188	cAt/cTt	0	0.502	TTTCTTCCGATGTCGATGTTC
SLC20A2	6575	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	42297083	42297083	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	170	122			ENST00000342228.3:c.819G>A	p.Glu273=	p.E273=	ENST00000342228	NM_006749.4	273	gaG/gaA	0	0.517	CACCTGGTAGCTCTTTAAATA
XIAP	331	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	123034427	123034427	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5	32			ENST00000355640.3:c.1184A>G	p.Glu395Gly	p.E395G	ENST00000355640		395	gAa/gGa	0	0.368	ATAATGGAGGAAAAAATTCAG
VPS13D	55187	broad.mit.edu;ucsc.edu	GRCh37	1	12439544	12439544	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	60	40			ENST00000358136.3:c.11084A>G	p.Tyr3695Cys	p.Y3695C	ENST00000358136	NM_015378.2	3695	tAc/tGc	0	0.498	TTTTCCAGATACGAGCCACTG
PBX2	5089	broad.mit.edu;ucsc.edu	GRCh37	6	32157564	32157564	+	synonymous_variant	Silent	SNP	C	C	A	rs151067717		TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	66	32			ENST00000375050.4:c.129G>T	p.Gly43=	p.G43=	ENST00000375050	NM_002586.4	43	ggG/ggT	0	0.711	CTCCCGGGACCCCCCCGCTAC
C12orf55	144535	broad.mit.edu;ucsc.edu	GRCh37	12	97151344	97151344	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	16	5			ENST00000524981.4:c.8018C>T	p.Ser2673Leu	p.S2673L	ENST00000524981		2673	tCa/tTa	0	0.303	ATAAAAATTTCAGGATCACCA
FAM212B	55924	broad.mit.edu;ucsc.edu	GRCh37	1	112270041	112270041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142952172		TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	44	35			ENST00000357260.5:c.443G>A	p.Arg148Gln	p.R148Q	ENST00000357260	NM_019099.4	148	cGg/cAg	0	0.587	ATTCCGGCCCCGGGACATCAA
UHRF1BP1	54887	broad.mit.edu;ucsc.edu	GRCh37	6	34827130	34827130	+	synonymous_variant	Silent	SNP	G	G	A	rs73419681	by1000genomes	TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	54	31			ENST00000192788.5:c.2997G>A	p.Glu999=	p.E999=	ENST00000192788	NM_017754.3	999	gaG/gaA	0	0.552	CTGGCAGGGAGACTGCTGTGA
H2AFX	3014	broad.mit.edu;hgsc.bcm.edu	GRCh37	11	118965808	118965809	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	191	73			ENST00000530167.1:c.296dupG	p.Gly100ArgfsTer131	p.G100Rfs*131	ENST00000530167	NM_002105.2	99	ggc/ggGc	0	0.693	TCGTCACGCCGCCCAGCAGCTT
ATRX	546	broad.mit.edu;hgsc.bcm.edu	GRCh37	X	76937745	76937745	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8	52			ENST00000373344.5:c.3003delA	p.Val1002Ter	p.V1002*	ENST00000373344	NM_000489.3	1001	aaA/aa	0	0.338	TTTTAATTACTTTTTTCTTAA
PIK3R1	5295	hgsc.bcm.edu	GRCh37	5	67593256	67593256	+	missense_variant	Missense_Mutation	SNP	A	A	C			TCGA-HT-7604-01	TCGA-HT-7604-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93	18			ENST00000274335.5:c.2002A>C	p.Lys668Gln	p.K668Q	ENST00000274335		668	Aag/Cag	0	0.423	CGGCGAAGTAAAGCATTGTGT
IDI1	3422	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	1089327	1089327	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HW-7487-01	TCGA-HW-7487-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	27	22			ENST00000381344.3:c.320T>C	p.Leu107Ser	p.L107S	ENST00000381344	NM_004508.2	107	tTg/tCg	0	0.348	AGCTCGATGCAATAATCCTGA
OR4K15	81127	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	14	20444378	20444378	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HW-7487-01	TCGA-HW-7487-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	100	42			ENST00000305051.5:c.701C>T	p.Ser234Phe	p.S234F	ENST00000305051	NM_001005486.1	234	tCc/tTc	0	0.453	TCTCTGAGTTCCTTTCTCCTC
CHD8	57680	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	14	21868155	21868155	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HW-7487-01	TCGA-HW-7487-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	209	80			ENST00000399982.2:c.4802G>A	p.Gly1601Glu	p.G1601E	ENST00000399982	NM_001170629.1	1601	gGg/gAg	0	0.423	AATCGCACCCCCTAACACCTT
AHNAK2	113146	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	14	105420366	105420366	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HW-7487-01	TCGA-HW-7487-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52	8			ENST00000333244.5:c.1422C>T	p.Gly474=	p.G474=	ENST00000333244	NM_138420.2	474	ggC/ggT	0	0.522	CAATCTGTGTGCCTCCTTCGG
SPTBN5	51332	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	42164528	42164528	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HW-7487-01	TCGA-HW-7487-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	20	8			ENST00000320955.6:c.5137C>T	p.Arg1713Trp	p.R1713W	ENST00000320955	NM_016642.3	1713	Cgg/Tgg	0	0.637	TGCAGTGCCCGCAGCTGCTCC
LAMA3	3909	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	18	21330907	21330907	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HW-7487-01	TCGA-HW-7487-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	100	55			ENST00000313654.9:c.710G>A	p.Arg237His	p.R237H	ENST00000313654	NM_198129.1	237	cGt/cAt	0	0.393	ATAAACGGTCGTCCAGGTGCA
MISP	126353	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	757295	757295	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-HW-7487-01	TCGA-HW-7487-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21	12			ENST00000215582.6:c.349G>C	p.Glu117Gln	p.E117Q	ENST00000215582	NM_173481.2	117	Gag/Cag	0	0.667	AGAGGACGGGGAGGACAAGGA
CIC	23152	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	42791758	42791758	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HW-7487-01	TCGA-HW-7487-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	16	21			ENST00000575354.2:c.644G>A	p.Arg215Gln	p.R215Q	ENST00000575354	NM_015125.3	215	cGg/cAg	0	0.612	AAGCGGCACCGGGCCCTGGTC
NLRP9	338321	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	56249567	56249567	+	synonymous_variant	Silent	SNP	C	C	A			TCGA-HW-7487-01	TCGA-HW-7487-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	180	196			ENST00000332836.2:c.174G>T	p.Leu58=	p.L58=	ENST00000332836	NM_176820.2	58	ctG/ctT	0	0.458	GTTTGTCCAGCAGCTTTGCTA
UMODL1	89766	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	21	43519136	43519136	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HW-7487-01	TCGA-HW-7487-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62	33			ENST00000408989.2:c.1032C>T	p.Val344=	p.V344=	ENST00000408989	NM_173568.3	344	gtC/gtT	0	0.542	CTTTCCATGTCCGGGTTTACC
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	179433152	179433152	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HW-7487-01	TCGA-HW-7487-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	43	8			ENST00000589042.1:c.77707G>A	p.Val25903Ile	p.V25903I	ENST00000589042	NM_001267550.1	25903	Gtc/Atc	0	0.403	TCAGCACTGACGTCATCAAAT
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HW-7487-01	TCGA-HW-7487-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	77	19			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
ITPR1	3708	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	4725122	4725122	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HW-7487-01	TCGA-HW-7487-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	149	63			ENST00000302640.8:c.3169C>T	p.Arg1057Cys	p.R1057C	ENST00000302640	NM_001168272.1	1057	Cgt/Tgt	0	0.582	AACCTTTCTCCGTGTCCTGCT
MYLK	4638	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	123419711	123419711	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HW-7487-01	TCGA-HW-7487-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	81	34			ENST00000360304.3:c.2604C>T	p.Asp868=	p.D868=	ENST00000360304	NM_053025.3	868	gaC/gaT	0	0.652	CCCCTCGCACGTCCTCGCCGT
MARCH1	55016	hgsc.bcm.edu;broad.mit.edu	GRCh37	4	164450155	164450155	+	synonymous_variant	Silent	SNP	G	G	C			TCGA-HW-7487-01	TCGA-HW-7487-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	51	3			ENST00000503008.1:c.615C>G	p.Ala205=	p.A205=	ENST00000503008	NM_001166373.1	205	gcC/gcG	0	0.438	TGAAGCCAATGGCTACCACAA
TIFAB	497189	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	134785348	134785348	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HW-7487-01	TCGA-HW-7487-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	131	51			ENST00000537858.1:c.282G>A	p.Leu94=	p.L94=	ENST00000537858	NM_001099221.1	94	ctG/ctA	0	0.607	GGACCTGCTCCAGGTACCTCA
TRPC7	57113	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	135693009	135693009	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HW-7487-01	TCGA-HW-7487-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	53	37			ENST00000513104.1:c.67C>T	p.Arg23Cys	p.R23C	ENST00000513104	NM_020389.2	23	Cgc/Tgc	0	0.587	ATGGCCTGGCGACGGCCCTTC
SSPO	23145	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	149486800	149486800	+	non_coding_transcript_exon_variant	RNA	SNP	C	C	T			TCGA-HW-7487-01	TCGA-HW-7487-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30	15			ENST00000378016.2:n.4574C>T		*1525*	ENST00000378016				0	0.682	GATGAGGGGCCGGGACACTGC
CDKN2C	1031	broad.mit.edu;ucsc.edu	GRCh37	1	51439758	51439758	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HW-7487-01	TCGA-HW-7487-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9	8			ENST00000262662.1:c.323A>G	p.His108Arg	p.H108R	ENST00000262662		108	cAc/cGc	0	0.552	CTGCCCTTGCACTTGGCTGCC
DAO	1610	broad.mit.edu;ucsc.edu	GRCh37	12	109294236	109294236	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HW-7487-01	TCGA-HW-7487-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91	18			ENST00000228476.3:c.969C>T	p.Ala323=	p.A323=	ENST00000228476	NM_001917.4	323	gcC/gcT	0	0.572	GGGGATGTGCCCTGGAGGCAG
FUBP1	8880	broad.mit.edu;hgsc.bcm.edu	GRCh37	1	78426058	78426059	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T			TCGA-HW-7487-01	TCGA-HW-7487-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6	13			ENST00000370768.2:c.1466dupA	p.Tyr489Ter	p.Y489*	ENST00000370768	NM_003902.3	489	tat/taAt	0	0.545	GTCCAGGATTATAAGGTGCAGG
ATAD1	84896	hgsc.bcm.edu;broad.mit.edu	GRCh37	10	89536119	89536119	+	missense_variant	Missense_Mutation	SNP	T	T	G			TCGA-FG-6690-01	TCGA-FG-6690-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	220	13			ENST00000308448.7:c.649A>C	p.Met217Leu	p.M217L	ENST00000308448	NM_032810.2	217	Atg/Ctg	0	0.378	CAGAGACTCATAAACTGAGCT
NPAT	4863	hgsc.bcm.edu;broad.mit.edu	GRCh37	11	108043929	108043929	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-FG-6690-01	TCGA-FG-6690-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	131	9			ENST00000278612.8:c.1782T>C	p.Asn594=	p.N594=	ENST00000278612	NM_002519.2	594	aaT/aaC	0	0.313	TATCTTGGCAATTTGATAGCT
NCAM1	4684	hgsc.bcm.edu;broad.mit.edu	GRCh37	11	113076288	113076288	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-FG-6690-01	TCGA-FG-6690-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	100	7			ENST00000524665.1:c.567G>A	p.Arg189=	p.R189=	ENST00000524665	NM_000615.6	189	cgG/cgA	0	0.507	AGGAGTTCCGGGAGGGGGAAG
KRT76	51350	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	53169301	53169301	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-FG-6690-01	TCGA-FG-6690-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	115	80			ENST00000332411.2:c.686G>A	p.Ser229Asn	p.S229N	ENST00000332411	NM_015848.4	229	aGc/aAc	0	0.557	AGGCTCCAGGCTGCTGGGCCC
REM2	161253	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	14	23354069	23354069	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-FG-6690-01	TCGA-FG-6690-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	94	14			ENST00000267396.4:c.290C>T	p.Ser97Leu	p.S97L	ENST00000267396	NM_173527.2	97	tCg/tTg	0	0.612	TCCTCTGGCTCGTCTGACTCC
CDC42BPB	9578	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	14	103430859	103430859	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-FG-6690-01	TCGA-FG-6690-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	63	16			ENST00000361246.2:c.2706C>T	p.Asp902=	p.D902=	ENST00000361246	NM_006035.3	902	gaC/gaT	0	0.652	TGAGGTTGGCGTCCTTGACCT
NDN	4692	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	23932264	23932264	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-FG-6690-01	TCGA-FG-6690-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	27	7			ENST00000331837.4:c.101C>T	p.Pro34Leu	p.P34L	ENST00000331837	NM_002487.2	34	cCg/cTg	0	0.692	GGTCGCGGACGGAGGAACCCC
ITGA11	22801	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	68643096	68643096	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-FG-6690-01	TCGA-FG-6690-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	86	29			ENST00000315757.7:c.919G>A	p.Gly307Arg	p.G307R	ENST00000315757	NM_001004439.1	307	Ggg/Agg	0	0.502	GGATTGATCCCCCTGCGGTTG
ATXN2L	11273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	28846974	28846974	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-FG-6690-01	TCGA-FG-6690-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	72	9			ENST00000395547.2:c.2790T>C	p.Pro930=	p.P930=	ENST00000395547	NM_148414.2	930	ccT/ccC	0	0.662	CACCGGGACCTTCTGCCCAGT
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-FG-6690-01	TCGA-FG-6690-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76	46			ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	0	0.572	GGAACTGTTACACATGTAGTT
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A			TCGA-FG-6690-01	TCGA-FG-6690-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35	27			ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	0	0.552	CCTTCCACTCGGATAAGATGC
MUC16	94025	hgsc.bcm.edu;broad.mit.edu	GRCh37	19	9086351	9086351	+	missense_variant	Missense_Mutation	SNP	T	T	A			TCGA-FG-6690-01	TCGA-FG-6690-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	137	8			ENST00000397910.4:c.5464A>T	p.Thr1822Ser	p.T1822S	ENST00000397910	NM_024690.2	1822	Act/Tct	0	0.483	ATTGATGGAGTTGGAGATGGA
SMARCA4	6597	hgsc.bcm.edu;broad.mit.edu	GRCh37	19	11098500	11098500	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-FG-6690-01	TCGA-FG-6690-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7	11			ENST00000344626.4:c.1018G>A	p.Ala340Thr	p.A340T	ENST00000344626	NM_003072.3	340	Gcg/Acg	0	0.746	GGCCCAGCCCGCGCCCATGGT
ATP4A	495	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	36054521	36054521	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A			TCGA-FG-6690-01	TCGA-FG-6690-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	46	9			ENST00000262623.3:c.11C>T	p.Ala4Val	p.A4V	ENST00000262623	NM_000704.2	4	gCc/gTc	0	0.652	CCCACTCACGGCCTTCCCCAT
PANK4	55229	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	2440330	2440330	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-FG-6690-01	TCGA-FG-6690-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24	19			ENST00000378466.3:c.2278C>T	p.Arg760Trp	p.R760W	ENST00000378466	NM_018216.1	760	Cgg/Tgg	0	0.622	CTGAAGAGCCGGCCGCCCAGC
ZZZ3	26009	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	78041829	78041829	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-FG-6690-01	TCGA-FG-6690-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68	39			ENST00000370801.3:c.2255C>T	p.Pro752Leu	p.P752L	ENST00000370801	NM_015534.4	752	cCg/cTg	0	0.378	ATACACTGGCGGTTCATGTGA
RBMXL1	494115	hgsc.bcm.edu;broad.mit.edu	GRCh37	1	89448635	89448635	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-FG-6690-01	TCGA-FG-6690-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	301	19			ENST00000399794.2:c.875G>A	p.Arg292His	p.R292H	ENST00000399794	NM_001162536.2	292	cGt/cAt	0	0.483	TGGAGCACTACGTGAGTTACC
ZNF831	128611	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	20	57769660	57769660	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-FG-6690-01	TCGA-FG-6690-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24	25			ENST00000371030.2:c.3586G>A	p.Ala1196Thr	p.A1196T	ENST00000371030	NM_178457.2	1196	Gcg/Acg	0	0.637	CCCTCTGCCCGCGGAGCAGAA
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-FG-6690-01	TCGA-FG-6690-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75	24			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
MSX2	4488	hgsc.bcm.edu;broad.mit.edu	GRCh37	5	174156254	174156254	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-FG-6690-01	TCGA-FG-6690-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78	4			ENST00000239243.6:c.472G>A	p.Glu158Lys	p.E158K	ENST00000239243	NM_002449.4	158	Gag/Aag	0	0.552	CCTCGCCCTGGAGCGCAAGTT
DNAH8	1769	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	38976646	38976646	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-FG-6690-01	TCGA-FG-6690-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	158	87			ENST00000359357.3:c.12620A>G	p.Lys4207Arg	p.K4207R	ENST00000359357		4207	aAa/aGa	0	0.423	ATTCAACCCAAAGAGAGTGGA
PHF10	55274	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	170112612	170112612	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-FG-6690-01	TCGA-FG-6690-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	117	10			ENST00000339209.4:c.827A>G	p.Tyr276Cys	p.Y276C	ENST00000339209	NM_133325.2	276	tAt/tGt	0	0.438	TAATGGCAGATACCGCAGCTC
TNFSF15	9966	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	117552881	117552881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150498686		TCGA-FG-6690-01	TCGA-FG-6690-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62	10			ENST00000374045.4:c.607G>A	p.Glu203Lys	p.E203K	ENST00000374045	NM_005118.3	203	Gaa/Aaa	0	0.527	CTACCTACTTCGCATACAGAC
ATRX	546	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	76939522	76939522	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs122445109		TCGA-FG-6690-01	TCGA-FG-6690-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64	241			ENST00000373344.5:c.1226T>A	p.Leu409Ter	p.L409*	ENST00000373344	NM_000489.3	409	tTg/tAg	0	0.363	GTCTTCTTCCAATGCAAGATG
CCNB1IP1	57820	broad.mit.edu;ucsc.edu	GRCh37	14	20779861	20779861	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-FG-6690-01	TCGA-FG-6690-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	103	8			ENST00000398169.3:c.682G>A	p.Asp228Asn	p.D228N	ENST00000398169		228	Gat/Aat	0	0.398	CCATCTCCATCGCCCCGATTT
RIOK3	8780	broad.mit.edu;ucsc.edu	GRCh37	18	21057190	21057190	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs56187215		TCGA-FG-6690-01	TCGA-FG-6690-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	70	53			ENST00000339486.3:c.1302C>A	p.His434Gln	p.H434Q	ENST00000339486	NM_003831.3	434	caC/caA	0	0.413	CCCACCCTCACGGCCTGGAGT
HSP90AB2P	391634	broad.mit.edu;ucsc.edu	GRCh37	4	13339305	13339305	+	non_coding_transcript_exon_variant	RNA	SNP	A	A	T			TCGA-FG-6690-01	TCGA-FG-6690-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21	6			ENST00000507090.2:n.1200A>T		*400*	ENST00000507090				0	0.423	AAAATCTTCAAAGTCATTCAC
MYH2	4620	broad.mit.edu;ucsc.edu	GRCh37	17	10451106	10451106	+	missense_variant	Missense_Mutation	SNP	T	T	A			TCGA-FG-6690-01	TCGA-FG-6690-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	122	83			ENST00000245503.5:c.132A>T	p.Lys44Asn	p.K44N	ENST00000245503	NM_017534.5	44	aaA/aaT	0	0.537	CAAAGGATTCTTTGGGCTCCG
MS4A3	932	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	59830060	59830060	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-8108-01	TCGA-HT-8108-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	63	51			ENST00000278865.3:c.276G>A	p.Pro92=	p.P92=	ENST00000278865	NM_006138.4	92	ccG/ccA	0	0.423	CAGGCTACCCGATTTGGGGTG
IL18	3606	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	112014361	112014361	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-HT-8108-01	TCGA-HT-8108-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	12	6			ENST00000280357.7:c.540G>T	p.Leu180Phe	p.L180F	ENST00000280357	NM_001562.3	180	ttG/ttT	0	0.388	ATCTATCCCCCAATTCATCCT
CADM1	23705	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	115109342	115109342	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-8108-01	TCGA-HT-8108-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28	28			ENST00000452722.3:c.302A>G	p.Asn101Ser	p.N101S	ENST00000452722	NM_014333.3	101	aAt/aGt	0	0.393	GCTAGAAAAATTCAGCAACTG
KERA	11081	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	91445220	91445220	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-8108-01	TCGA-HT-8108-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	32	13			ENST00000266719.3:c.962A>G	p.His321Arg	p.H321R	ENST00000266719	NM_007035.3	321	cAt/cGt	0	0.438	GTAGCGAAGATGAGGTCCATA
CDK10	8558	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	89755723	89755723	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-8108-01	TCGA-HT-8108-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	48	30			ENST00000353379.7:c.151G>A	p.Gly51Ser	p.G51S	ENST00000353379	NM_052988.4	51	Ggc/Agc	0	0.582	GGGTACCTACGGCATTGTGTG
GNAL	2774	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	18	11880999	11880999	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-8108-01	TCGA-HT-8108-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	53	31			ENST00000334049.6:c.1242G>A	p.Thr414=	p.T414=	ENST00000334049	NM_182978.3	414	acG/acA	0	0.622	GGATCAGCACGGCCACCGGTG
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	179593263	179593263	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-8108-01	TCGA-HT-8108-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15	5			ENST00000589042.1:c.19390G>A	p.Gly6464Arg	p.G6464R	ENST00000589042	NM_001267550.1	6464	Gga/Aga	0	0.398	CTACTGCTTCCGAAGTCATTT
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HT-8108-01	TCGA-HT-8108-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	54	35			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
EIF4A2	1974	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	186501406	186501406	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-HT-8108-01	TCGA-HT-8108-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	100	59			ENST00000323963.5:c.7G>T	p.Gly3Cys	p.G3C	ENST00000323963		3	Ggt/Tgt	0	0.572	GATCATGTCTGGTGGCTCCGC
BBS7	55212	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	122756377	122756377	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-HT-8108-01	TCGA-HT-8108-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47	18			ENST00000264499.4:c.1433C>A	p.Pro478His	p.P478H	ENST00000264499	NM_176824.2	478	cCc/cAc	0	0.393	ACAGGTTTTGGGTTGAATTCT
ROPN1L	83853	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	10461352	10461352	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-8108-01	TCGA-HT-8108-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99	60			ENST00000503804.1:c.474C>T	p.Gly158=	p.G158=	ENST00000503804		158	ggC/ggT	0	0.567	ATCCGGAGGGCGGGCCCGCTC
SIM1	6492	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	100911318	100911318	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-8108-01	TCGA-HT-8108-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	162	32			ENST00000369208.3:c.27G>A	p.Ala9=	p.A9=	ENST00000369208		9	gcG/gcA	0	0.423	TCCTAGTCCGCGCAGCATTTT
OPHN1	4983	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	67414334	67414334	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-HT-8108-01	TCGA-HT-8108-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28	19			ENST00000355520.5:c.1111C>G	p.His371Asp	p.H371D	ENST00000355520	NM_002547.2	371	Cac/Gac	0	0.348	ATAGGGCTGTGGTAGATCTAC
IRS4	8471	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	107979043	107979043	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-HT-8108-01	TCGA-HT-8108-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75	30			ENST00000372129.2:c.532G>C	p.Ala178Pro	p.A178P	ENST00000372129	NM_003604.2	178	Gcg/Ccg	0	0.612	GCCACCATCGCGAAGTATTCG
TENM1	10178	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	123518058	123518058	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-8108-01	TCGA-HT-8108-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67	47			ENST00000422452.2:c.6723G>A	p.Leu2241=	p.L2241=	ENST00000422452	NM_001163279.1	2241	ctG/ctA	0	0.458	AGGCTTTCTGCAGCAGGCCAT
RENBP	5973	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	153208518	153208518	+	missense_variant	Missense_Mutation	SNP	T	T	G			TCGA-HT-8108-01	TCGA-HT-8108-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	20	21			ENST00000393700.3:c.476A>C	p.Glu159Ala	p.E159A	ENST00000393700	NM_002910.5	159	gAg/gCg	0	0.711	ATCCATCATCTCCACCGCTTC
SYNE1	23345	broad.mit.edu;ucsc.edu	GRCh37	6	152485384	152485384	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-8108-01	TCGA-HT-8108-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	25	57			ENST00000367255.5:c.23704G>A	p.Ala7902Thr	p.A7902T	ENST00000367255	NM_182961.3	7902	Gct/Act	0	0.502	TCGATGTGAGCGAGCCAGGTC
IL36B	27177	broad.mit.edu;ucsc.edu	GRCh37	2	113788702	113788702	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-8108-01	TCGA-HT-8108-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	43	17			ENST00000259213.4:c.44G>A	p.Arg15His	p.R15H	ENST00000259213	NM_014438.4	15	cGt/cAt	0	0.478	TCGAGAATCACGAATAGCATA
TP53	7157	broad.mit.edu;hgsc.bcm.edu	GRCh37	17	7578471	7578471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs137852790		TCGA-HT-8108-01	TCGA-HT-8108-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28	70			ENST00000269305.4:c.459delC	p.Gly154AlafsTer16	p.G154Afs*16	ENST00000269305	NM_001126112.2	153	ccC/cc	0	0.612	CGCGGGTGCCGGGCGGGGGTG
ATRX	546	broad.mit.edu;hgsc.bcm.edu	GRCh37	X	76813062	76813063	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG			TCGA-HT-8108-01	TCGA-HT-8108-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	101	65			ENST00000373344.5:c.6557_6558dupCT	p.Phe2187LeufsTer16	p.F2187Lfs*16	ENST00000373344	NM_000489.3	2186	-/CT	0	0.347	ACAACTCGAAAAGACAGTGACT
KNDC1	85442	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	135038195	135038195	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	59	25			ENST00000304613.3:c.5051C>T	p.Ala1684Val	p.A1684V	ENST00000304613		1684	gCg/gTg	0	0.597	CAGGTGCACGCGTTCCAGGAG
OR52B6	340980	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	5602864	5602864	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340	43			ENST00000345043.2:c.758G>A	p.Arg253His	p.R253H	ENST00000345043	NM_001005162.2	253	cGc/cAc	0	0.507	CAAGATGCCCGCTCCAAGGCC
MS4A6E	245802	hgsc.bcm.edu;broad.mit.edu	GRCh37	11	60105367	60105367	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	199	14			ENST00000300182.4:c.301G>T	p.Asp101Tyr	p.D101Y	ENST00000300182	NM_139249.2	101	Gat/Tat	0	0.403	TCTTTCTTATGATTATCATTC
AHNAK	79026	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	62299210	62299210	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	348	280			ENST00000378024.4:c.2679G>A	p.Glu893=	p.E893=	ENST00000378024	NM_001620.2	893	gaG/gaA	0	0.517	CTTCTGGGCCCTCTGCTTTGA
CWF19L2	143884	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	107224323	107224323	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79	50			ENST00000282251.5:c.2012A>G	p.Gln671Arg	p.Q671R	ENST00000282251	NM_152434.2	671	cAa/cGa	0	0.393	TTTTTCCATTTGTGCAGCAAG
KSR2	283455	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	118016978	118016978	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52	7			ENST00000339824.5:c.1271C>T	p.Thr424Met	p.T424M	ENST00000339824		424	aCg/aTg	0	0.468	GACTGTGCACGTCTGAGACAT
LMO7	4008	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	13	76382215	76382215	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	59	26			ENST00000465261.2:c.1097G>A	p.Gly366Glu	p.G366E	ENST00000465261	NM_015842.2	366	gGa/gAa	0	0.498	TGGAAACTGGGAACTACCGTG
CYP1A1	1543	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	75012968	75012968	+	synonymous_variant	Silent	SNP	G	G	C			TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	141	35			ENST00000379727.3:c.1401C>G	p.Val467=	p.V467=	ENST00000379727		467	gtC/gtG	0	0.542	GGAAGAGAAAGACCTCCCAGC
IDH2	3418	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913503		TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88	65			ENST00000330062.3:c.515G>T	p.Arg172Met	p.R172M	ENST00000330062	NM_002168.2	172	aGg/aTg	0	0.632	ATGGGCGTGCCTGCCAATGGT
CDH5	1003	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	66436644	66436644	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17	5			ENST00000341529.3:c.1927G>A	p.Val643Ile	p.V643I	ENST00000341529	NM_001795.3	643	Gtc/Atc	0	0.711	CGAGCAGCTGGTCACCTACGA
KRT33B	3884	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	39521763	39521763	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40	27			ENST00000251646.3:c.631G>A	p.Val211Met	p.V211M	ENST00000251646	NM_002279.4	211	Gtg/Atg	0	0.522	TCCACCTCCACGTTGAGGCGG
ELL	8178	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	18557617	18557617	+	synonymous_variant	Silent	SNP	G	G	A	rs73923115	byFrequency	TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	55	13			ENST00000262809.4:c.1473C>T	p.Asn491=	p.N491=	ENST00000262809	NM_006532.3	491	aaC/aaT	0	0.572	TGCAGGTTCCGTTTAAACCTA
PRODH2	58510	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	36302867	36302867	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14	24			ENST00000301175.3:c.822G>A	p.Gly274=	p.G274=	ENST00000301175	NM_021232.1	274	ggG/ggA	0	0.597	TCCTTACCTGCCCAGAGTCCA
KLK4	9622	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	51411835	51411835	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T			TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	85	8			ENST00000324041.1:c.475G>A	p.Gly159Ser	p.G159S	ENST00000324041	NM_004917.3	159	Ggc/Agc	0	0.637	GTGAGCTCACCGTTCGCCAGC
HRNR	388697	hgsc.bcm.edu;broad.mit.edu	GRCh37	1	152193228	152193228	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	317	15			ENST00000368801.2:c.877T>C	p.Ser293Pro	p.S293P	ENST00000368801	NM_001009931.2	293	Tct/Cct	0	0.607	TGGCCCAAAGACTGACGGGAA
SELE	6401	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	169698637	169698637	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	103	87			ENST00000333360.7:c.893C>T	p.Thr298Met	p.T298M	ENST00000333360	NM_000450.2	298	aCg/aTg	0	0.443	ACCTTTACACGTTGGCTTCTC
IL1RL2	8808	hgsc.bcm.edu;broad.mit.edu	GRCh37	2	102805614	102805614	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	151	10			ENST00000264257.2:c.137C>A	p.Pro46His	p.P46H	ENST00000264257	NM_003854.2	46	cCc/cAc	0	0.378	ACATTCCCTCCCATAACATCT
NEB	4703	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	152521900	152521900	+	missense_variant	Missense_Mutation	SNP	T	T	A			TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41	33			ENST00000397345.3:c.5185A>T	p.Met1729Leu	p.M1729L	ENST00000397345	NM_001164508.1	1729	Atg/Ttg	0	0.507	ATTGTGTCCATGGCGTAAGTG
KLHL30	377007	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	239051515	239051515	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18	6			ENST00000409223.1:c.850G>A	p.Ala284Thr	p.A284T	ENST00000409223		284	Gca/Aca	0	0.672	GGAGGAGGAGGCAGGTGAGGA
SI	6476	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	164776970	164776970	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs148511215	by1000genomes	TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	102	16			ENST00000264382.3:c.1264T>C	p.Tyr422His	p.Y422H	ENST00000264382	NM_001041.3	422	Tat/Cat	0	0.323	ATGATGACATATTTCTGTCCA
FSTL5	56884	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	162577528	162577528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T			TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	106	18			ENST00000306100.5:c.846G>A	p.Trp282Ter	p.W282*	ENST00000306100	NM_001128427.2	282	tgG/tgA	0	0.353	TGTTCCTTTTCCAGATAATGG
PSD3	23362	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	18725224	18725224	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs62636654		TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	111	73			ENST00000327040.8:c.1594A>G	p.Ile532Val	p.I532V	ENST00000327040	NM_015310.3	532	Atc/Gtc	0	0.507	TTCGTGTAGATGGAGTCGCTG
KCNU1	157855	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	36671795	36671795	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	63	8			ENST00000399881.3:c.803A>G	p.Tyr268Cys	p.Y268C	ENST00000399881	NM_001031836.2	268	tAc/tGc	0	0.433	GAGTCAATTTACCTGGTCATG
KLHL9	55958	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	21333865	21333865	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	145	91			ENST00000359039.4:c.994C>T	p.Pro332Ser	p.P332S	ENST00000359039		332	Cca/Tca	0	0.418	GCATCCATTGGGGCTAAAGAT
SIT1	27240	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	35650242	35650242	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T			TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78	55			ENST00000259608.3:c.296G>A	p.Gly99Glu	p.G99E	ENST00000259608	NM_014450.2	99	gGa/gAa	0	0.627	AGACAGCCGTCCTGGGACGGG
ARSE	415	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	2867631	2867631	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	77	9			ENST00000381134.3:c.568C>T	p.Arg190Cys	p.R190C	ENST00000381134	NM_000047.2	190	Cgt/Tgt	0	0.527	AGGTTGACACGCTTCTCTGAG
MAGEB2	4113	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	30237371	30237371	+	missense_variant	Missense_Mutation	SNP	A	A	T			TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	63	14			ENST00000378988.4:c.674A>T	p.Glu225Val	p.E225V	ENST00000378988	NM_002364.4	225	gAa/gTa	0	0.483	GAGATCTGGGAATTCCTGAAT
PGRMC1	10857	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	118370561	118370561	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	31	16			ENST00000217971.7:c.235C>T	p.Arg79Trp	p.R79W	ENST00000217971	NM_006667.3	79	Cgg/Tgg	0	0.711	CGCCGAGCTGCGGCGCTTCGA
LAMP2	3920	hgsc.bcm.edu;broad.mit.edu	GRCh37	X	119581704	119581704	+	stop_gained	Nonsense_Mutation	SNP	G	G	A			TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258	19			ENST00000434600.2:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000434600	NM_001122606.1	245	Cag/Tag	0	0.403	ACCTTATCCTGAGTGATGTTC
NAIP	4671	broad.mit.edu;ucsc.edu	GRCh37	5	70308387	70308387	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98	65			ENST00000517649.1:c.356G>A	p.Arg119Lys	p.R119K	ENST00000517649	NM_004536.2	119	aGg/aAg	0	0.473	TGGATGAAACCTCTTGTGGTC
HTR7P1	93164	broad.mit.edu;ucsc.edu	GRCh37	12	13155006	13155006	+	non_coding_transcript_exon_variant	RNA	SNP	G	G	C			TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15	4			ENST00000331998.1:n.1458G>C		*486*	ENST00000331998				0	0.483	CGTACCCTATGAGGCAGAAGG
PDHA1	5160	broad.mit.edu;ucsc.edu	GRCh37	X	19368118	19368118	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98	75			ENST00000379806.5:c.295G>C	p.Gly99Arg	p.G99R	ENST00000379806	NM_001173454.1	99	Ggg/Cgg	0	0.453	CAGGGAGGATGGGCTCAAATA
BRWD1	54014	broad.mit.edu;ucsc.edu	GRCh37	21	40590181	40590181	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs75547980		TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	145	23			ENST00000333229.2:c.3556G>A	p.Ala1186Thr	p.A1186T	ENST00000333229	NM_018963.4	1186	Gca/Aca	0	0.368	ACAGGGCCTGCAAAAGCTGCT
CIC	23152	broad.mit.edu;hgsc.bcm.edu	GRCh37	19	42795241	42795242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCCCCT			TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30	10			ENST00000575354.2:c.2324_2330dupCCCCTGC	p.Val778ProfsTer155	p.V778Pfs*155	ENST00000575354	NM_015125.3	774	gcg/gcGCCCCCTg	0	0.698	GGGGCCCCTGCGCCCCCTGCTG
BCOR	54880	broad.mit.edu;hgsc.bcm.edu	GRCh37	X	39933875	39933875	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-			TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	66	42			ENST00000378444.4:c.724delG	p.Glu242SerfsTer24	p.E242Sfs*24	ENST00000378444	NM_001123385.1	242	Gag/ag	0	0.577	AGAAAGCGCTCCCCATTGGTG
NOTCH1	4851	ucsc.edu	GRCh37	9	139418186	139418186	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-E1-5318-01	TCGA-E1-5318-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	16	2			ENST00000277541.6:c.386G>A	p.Cys129Tyr	p.C129Y	ENST00000277541	NM_017617.3	129	tGc/tAc	0	0.697	GCCGGGCGGGCAGCGGCACTT
KIAA1217	56243	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	24832988	24832988	+	stop_gained	Nonsense_Mutation	SNP	A	A	T			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	122	13			ENST00000376454.3:c.4789A>T	p.Lys1597Ter	p.K1597*	ENST00000376454	NM_019590.3	1597	Aag/Tag	0	0.463	TAAAACAGGGAAGAAGACTTT
AGAP5	729092	hgsc.bcm.edu;broad.mit.edu	GRCh37	10	75457306	75457306	+	stop_gained	Nonsense_Mutation	SNP	G	G	A			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	197	15			ENST00000374094.4:c.208C>T	p.Gln70Ter	p.Q70*	ENST00000374094	NM_001144000.1	70	Cag/Tag	0	0.592	GGCATCTCCTGGTCACGAATG
HELLS	3070	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	96352241	96352241	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	44	12			ENST00000348459.5:c.1941G>A	p.Gly647=	p.G647=	ENST00000348459	NM_018063.3	647	ggG/ggA	0	0.343	GGCTTGATGGGTCCATGTCTT
SLIT1	6585	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	98764460	98764460	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	65	15			ENST00000266058.4:c.3700G>A	p.Ala1234Thr	p.A1234T	ENST00000266058	NM_003061.2	1234	Gcc/Acc	0	0.602	CTGTAGATGGCAGAGCTGGGG
MAP3K12	7786	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	53877509	53877509	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64	8			ENST00000547035.1:c.1359-2A>T		p.X453_splice	ENST00000547035				0	0.507	AGGGCGTGTCTGCAACGGGCA
SMUG1	23583	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	54577582	54577582	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149806805	byFrequency	TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	55	6			ENST00000508394.2:c.143C>T	p.Ser48Leu	p.S48L	ENST00000508394	NM_001243788.1	48	tCg/tTg	0	0.597	CACAGGCTCCGAAAACTGCAG
TBX5	6910	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	114793348	114793348	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	56	8			ENST00000310346.4:c.1546G>A	p.Asp516Asn	p.D516N	ENST00000310346	NM_000192.3	516	Gac/Aac	0	0.517	TAGCTATTGTCGCTCCACTCT
TRPM1	4308	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	31359319	31359319	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74	50			ENST00000542188.1:c.616G>A	p.Gly206Arg	p.G206R	ENST00000542188	NM_001252020.1	206	Gga/Aga	0	0.453	GGAGCAATTCCTATAGCACAA
SPPL2A	84888	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	51017471	51017471	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	120	52			ENST00000261854.5:c.1196G>C	p.Ser399Thr	p.S399T	ENST00000261854	NM_032802.3	399	aGt/aCt	0	0.313	GAGGCACACACTCATTACTGA
TPM1	7168	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	63336271	63336271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104894505		TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	25	9			ENST00000358278.3:c.160G>A	p.Glu54Lys	p.E54K	ENST00000358278	NM_001018006.1	54	Gaa/Aaa	0	0.562	CAAGGGCACCGAAGATGAACT
NEO1	4756	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	73428355	73428355	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	32	17			ENST00000339362.5:c.1002G>C	p.Glu334Asp	p.E334D	ENST00000339362		334	gaG/gaC	0	0.373	CTCAAGCAGAGCTTACAGTGC
SMAD2	4087	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	18	45422914	45422914	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	86	9			ENST00000262160.6:c.214A>G	p.Thr72Ala	p.T72A	ENST00000262160	NM_005901.5	72	Act/Gct	0	0.368	ACACATTTAGTATTACAGTTT
DAPK3	1613	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	3964722	3964722	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	133	17			ENST00000545797.2:c.330G>A	p.Ser110=	p.S110=	ENST00000545797		110	tcG/tcA	0	0.592	CCTCCGTCAGCGACTCCTTCT
C3	718	hgsc.bcm.edu;broad.mit.edu	GRCh37	19	6718386	6718386	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	148	10			ENST00000245907.6:c.305G>A	p.Arg102His	p.R102H	ENST00000245907	NM_000064.2	102	cGc/cAc	0	0.607	GAACTTGTTGCGCCCCTTTTC
ZNF878	729747	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	12154973	12154973	+	stop_gained	Nonsense_Mutation	SNP	G	G	A			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	34	13			ENST00000547628.1:c.1243C>T	p.Arg415Ter	p.R415*	ENST00000547628	NM_001080404.2	415	Cga/Tga	0	0.433	GTGTGAGTTCGTATGTGCTTT
NOTCH3	4854	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	15299837	15299837	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	32	9			ENST00000263388.2:c.1341C>T	p.Leu447=	p.L447=	ENST00000263388	NM_000435.2	447	ctC/ctT	0	0.667	CTATGCGGTCGAGGCACGTGG
TEAD2	8463	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	49845721	49845721	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35	27			ENST00000598810.1:c.1216G>A	p.Val406Ile	p.V406I	ENST00000598810	NM_001256661.1	406	Gtc/Atc	0	0.572	TTTTCCAGGACGCTGTTCATC
U2AF2	11338	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	56175034	56175034	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	106	10			ENST00000308924.4:c.666G>C	p.Gln222His	p.Q222H	ENST00000308924		222	caG/caC	0	0.567	TCCAGGGCCAGTCACTAAAGA
PRRC2C	23215	hgsc.bcm.edu;broad.mit.edu	GRCh37	1	171511013	171511013	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61	5			ENST00000338920.4:c.4402C>G	p.Pro1468Ala	p.P1468A	ENST00000338920	NM_015172.3	1468	Cca/Gca	0	0.428	GGCTCAAGAACCAGTTAATAC
BPIFB3	359710	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	20	31659936	31659936	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	87	15			ENST00000375494.3:c.1287C>T	p.Ser429=	p.S429=	ENST00000375494	NM_182658.1	429	agC/agT	0	0.532	AATGGCTCAGCCATGTGGTCG
COL18A1	80781	hgsc.bcm.edu;broad.mit.edu	GRCh37	21	46909433	46909433	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	12	10			ENST00000355480.5:c.2497A>G	p.Lys833Glu	p.K833E	ENST00000355480	NM_030582.3	833	Aag/Gag	0	0.706	GCCGGGGGCGAAGGTAAGCGC
PARVB	29780	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	22	44489821	44489821	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	104	49			ENST00000406477.3:c.225G>A	p.Gln75=	p.Q75=	ENST00000406477	NM_001003828.2	75	caG/caA	0	0.547	GTGACCTGCAGGAAGAAGGCA
TTN	7273	hgsc.bcm.edu;broad.mit.edu	GRCh37	2	179634978	179634978	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95	8			ENST00000589042.1:c.8450G>C	p.Ser2817Thr	p.S2817T	ENST00000589042	NM_001267550.1	2817	aGt/aCt	0	0.408	ATGGGAAACACTAACTTCAAA
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	65	20			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
NGEF	25791	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	233759484	233759484	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82	31			ENST00000264051.3:c.971T>C	p.Val324Ala	p.V324A	ENST00000264051	NM_019850.2	324	gTg/gCg	0	0.602	GACAGCCAGCACGTCCAGGAC
FLNB	2317	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	58097875	58097875	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	137	83			ENST00000490882.1:c.2576-1G>A		p.X859_splice	ENST00000490882	NM_001164317.1			0	0.522	TATCTTTCCAGGTGTGGAAAA
CRYBG3	131544	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	97596597	97596597	+	stop_gained	Nonsense_Mutation	SNP	C	C	T			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	22	12			ENST00000182096.4:c.715C>T	p.Gln239Ter	p.Q239*	ENST00000182096	NM_153605.3	239	Cag/Tag	0	0.468	CCCTGATGACCAGGAGAGCGT
ENAM	10117	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	71508741	71508741	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	63	32			ENST00000396073.3:c.1598C>T	p.Thr533Ile	p.T533I	ENST00000396073	NM_031889.2	533	aCt/aTt	0	0.413	GAATCAGAAACTAATCAGTCA
NAF1	92345	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	164050323	164050323	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	50	10			ENST00000274054.2:c.1211A>G	p.Gln404Arg	p.Q404R	ENST00000274054	NM_138386.2	404	cAg/cGg	0	0.458	TGAAGTCTCCTGAGATACCAT
FAT1	2195	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	187521295	187521295	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	46	6			ENST00000441802.2:c.11860G>A	p.Gly3954Ser	p.G3954S	ENST00000441802	NM_005245.3	3954	Ggc/Agc	0	0.483	CGGATGTGGCCACCAAAAAAC
MAML1	9794	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	179192669	179192669	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	46	5			ENST00000292599.3:c.658C>T	p.Pro220Ser	p.P220S	ENST00000292599	NM_014757.4	220	Cct/Tct	0	0.517	GAAGCAGGAGCCTGTCGAAGA
NOTCH4	4855	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	32166813	32166813	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	46	32			ENST00000375023.3:c.4425C>T	p.Arg1475=	p.R1475=	ENST00000375023	NM_004557.3	1475	cgC/cgT	0	0.677	CATGCTCTCGGCGTCGACGCC
NOTCH4	4855	hgsc.bcm.edu;broad.mit.edu	GRCh37	6	32190325	32190325	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69	8			ENST00000375023.3:c.414G>A	p.Ser138=	p.S138=	ENST00000375023	NM_004557.3	138	tcG/tcA	0	0.647	GTGGGCGGCCCGAGGCCTGGA
PNPLA1	285848	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	36262065	36262065	+	synonymous_variant	Silent	SNP	C	C	A			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	138	24			ENST00000394571.2:c.603C>A	p.Pro201=	p.P201=	ENST00000394571	NM_001145717.1	201	ccC/ccA	0	0.607	ACATCTGTCCCCGGGACTGCC
PPP2R5D	5528	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	42974286	42974286	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	130	76			ENST00000485511.1:c.191C>T	p.Pro64Leu	p.P64L	ENST00000485511	NM_001270476.1	64	cCg/cTg	0	0.622	AATAGCACGCCGCCCCCCACG
TTBK1	84630	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	43251409	43251409	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	32	26			ENST00000259750.4:c.2931G>A	p.Ala977=	p.A977=	ENST00000259750	NM_032538.1	977	gcG/gcA	0	0.697	GGGCCCGAGCGCCCCTGGAGA
ZNF292	23036	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	87943087	87943087	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	22	9			ENST00000369577.3:c.583A>G	p.Arg195Gly	p.R195G	ENST00000369577	NM_015021.1	195	Aga/Gga	0	0.308	GTTGGATATGAGAATTAAACA
RUNX1T1	862	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	92972658	92972658	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40	10			ENST00000436581.2:c.1660G>C	p.Asp554His	p.D554H	ENST00000436581		554	Gac/Cac	0	0.567	TTCTCCCAGTCTTTGTGCTGG
PLEC	5339	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	144995732	144995732	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	44	30			ENST00000322810.4:c.8668G>A	p.Ala2890Thr	p.A2890T	ENST00000322810	NM_201380.2	2890	Gct/Act	0	0.687	TCCTTCACAGCCTCGTTGACG
GNE	10020	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	36249251	36249251	+	synonymous_variant	Silent	SNP	G	G	A	rs147290887		TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	65	9			ENST00000396594.3:c.195C>T	p.Thr65=	p.T65=	ENST00000396594	NM_001128227.2	65	acC/acT	0	0.408	ACTCAGGTTCGGTTTTAATGC
ALDH1A1	216	hgsc.bcm.edu;ucsc.edu	GRCh37	9	75520933	75520933	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37	6			ENST00000297785.3:c.1374C>T	p.Gly458=	p.G458=	ENST00000297785	NM_000689.4	458	ggC/ggT	0	0.348	CACTTACCACGCCATAGCAAT
FPGS	2356	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	130570869	130570869	+	synonymous_variant	Silent	SNP	C	C	G			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29	20			ENST00000373247.2:c.855C>G	p.Ala285=	p.A285=	ENST00000373247	NM_004957.4	285	gcC/gcG	0	0.687	TGCTGGAGGCCCTCGAGGAAG
NOTCH1	4851	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	139412597	139412597	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10	9			ENST00000277541.6:c.1247G>T	p.Cys416Phe	p.C416F	ENST00000277541	NM_017617.3	416	tGc/tTc	0	0.672	ACCCAGCGAGCACTCATCCAC
FTSJ1	24140	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	48339829	48339829	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11	30			ENST00000348411.2:c.484G>T	p.Asp162Tyr	p.D162Y	ENST00000348411	NM_012280.2	162	Gat/Tat	0	0.602	CCGAGGCCGGGATGTGACGCT
LHFPL1	340596	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	111914414	111914414	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69	36			ENST00000371968.3:c.205C>T	p.Arg69Cys	p.R69C	ENST00000371968	NM_178175.3	69	Cgc/Tgc	0	0.592	CTGGCATAGCGCCCACATTCT
NSDHL	50814	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	152037637	152037637	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29	11			ENST00000370274.3:c.1099C>T	p.Arg367Cys	p.R367C	ENST00000370274	NM_015922.2	367	Cgc/Tgc	0	0.552	GCAGAGCTTTCGCCACCTGCG
ABI3BP	25890	broad.mit.edu;ucsc.edu	GRCh37	3	100523693	100523693	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40	13			ENST00000284322.5:c.1690C>T	p.Arg564Cys	p.R564C	ENST00000284322	NM_015429.3	564	Cgt/Tgt	0	0.398	GCAGTAACACGCTGGGGCACC
CRIP3	401262	broad.mit.edu;ucsc.edu	GRCh37	6	43275627	43275627	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35	4			ENST00000372569.3:c.146G>A	p.Gly49Glu	p.G49E	ENST00000372569	NM_206922.2	49	gGg/gAg	0	0.607	GTATGGCCTCCCATTGTGCTG
KPRP	448834	broad.mit.edu;ucsc.edu	GRCh37	1	152733157	152733157	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84	13			ENST00000368773.1:c.1093G>A	p.Ala365Thr	p.A365T	ENST00000368773	NM_001025231.1	365	Gcc/Acc	0	0.662	CTCCTGGGGCGCCTCCTGCCC
TTC12	54970	broad.mit.edu;ucsc.edu	GRCh37	11	113215006	113215006	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	126	73			ENST00000529221.1:c.998G>A	p.Arg333His	p.R333H	ENST00000529221	NM_017868.3	333	cGt/cAt	0	0.532	GAAAACCAGCGTGTGCTAGTG
THSD7B	80731	broad.mit.edu;ucsc.edu	GRCh37	2	137814593	137814593	+	stop_gained	Nonsense_Mutation	SNP	G	G	A			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	59	39			ENST00000272643.3:c.743G>A	p.Trp248Ter	p.W248*	ENST00000272643		248	tGg/tAg	0	0.413	GTTGGACCATGGAGTAAATGC
DIXDC1	85458	broad.mit.edu;ucsc.edu	GRCh37	11	111835363	111835363	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9	7			ENST00000440460.2:c.151C>T	p.Arg51Trp	p.R51W	ENST00000440460	NM_001037954.3	51	Cgg/Tgg	0	0.517	ACAAGATCTCCGGGATGGGGT
HFM1	164045	broad.mit.edu;hgsc.bcm.edu	GRCh37	1	91781979	91781980	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	20	29			ENST00000370425.3:c.2866dupA	p.Ile956AsnfsTer10	p.I956Nfs*10	ENST00000370425	NM_001017975.3	956	ata/aAta	0	0.292	TGTCTCTTCTATTTTTTTAAAG
KIAA1147	57189	broad.mit.edu;hgsc.bcm.edu	GRCh37	7	141362626	141362626	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2	10			ENST00000536163.1:c.1198delA	p.Ile400TyrfsTer16	p.I400Yfs*16	ENST00000536163	NM_001080392.1	400	Ata/ta	0	0.502	GTCTGAAATATCCGGTTGTTT
CIC	23152	broad.mit.edu;hgsc.bcm.edu	GRCh37	19	42797750	42797750	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-			TCGA-IK-8125-01	TCGA-IK-8125-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21	25			ENST00000575354.2:c.3804delA	p.Lys1268AsnfsTer34	p.K1268Nfs*34	ENST00000575354	NM_015125.3	1268	Aaa/aa	0	0.637	CCAGGCCAGCAAATTCCCCAG
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7880-01	TCGA-HT-7880-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91	10			ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	0	0.577	CTCCGGTTCATGCCGCCCATG
PTPN14	5784	hgsc.bcm.edu;broad.mit.edu	GRCh37	1	214557534	214557534	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7880-01	TCGA-HT-7880-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	124	10			ENST00000366956.5:c.1664C>T	p.Thr555Met	p.T555M	ENST00000366956	NM_005401.4	555	aCg/aTg	0	0.637	CATGTGGGCCGTGCTGTAGTT
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HT-7880-01	TCGA-HT-7880-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	56	15			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
PKN3	29941	hgsc.bcm.edu;broad.mit.edu	GRCh37	9	131475882	131475882	+	synonymous_variant	Silent	SNP	G	G	C			TCGA-HT-7880-01	TCGA-HT-7880-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88	6			ENST00000291906.4:c.1197G>C	p.Leu399=	p.L399=	ENST00000291906	NM_013355.3	399	ctG/ctC	0	0.632	GTCACCAACTGTCCCTCAGCC
ATRX	546	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	76937900	76937900	+	stop_gained	Nonsense_Mutation	SNP	T	T	A			TCGA-HT-7880-01	TCGA-HT-7880-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79	18			ENST00000373344.5:c.2848A>T	p.Lys950Ter	p.K950*	ENST00000373344	NM_000489.3	950	Aaa/Taa	0	0.358	GTTTTGGTTTTGAGATGCTTG
ATRX	546	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	76938788	76938788	+	synonymous_variant	Silent	SNP	G	G	T			TCGA-HT-7880-01	TCGA-HT-7880-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	115	19			ENST00000373344.5:c.1960C>A	p.Arg654=	p.R654=	ENST00000373344	NM_000489.3	654	Cga/Aga	0	0.393	GGGGATCTTCGAAGATCAGAT
AFF2	2334	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	148037448	148037448	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7880-01	TCGA-HT-7880-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	110	16			ENST00000370460.2:c.1873A>G	p.Thr625Ala	p.T625A	ENST00000370460	NM_002025.3	625	Aca/Gca	0	0.443	GTCTCAAAGGACAATTGGGAA
NF1	4763	broad.mit.edu	GRCh37	17	29562657	29562660	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-			TCGA-HT-7880-01	TCGA-HT-7880-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	226	20			ENST00000358273.4:c.3739_3742delTTTG	p.Phe1247IlefsTer18	p.F1247Ifs*18	ENST00000358273	NM_001042492.2	1246	cTGTTt/ct	0	0.412	CTGGTTACTCTGTTTGATTCTCGG
NAV2	89797	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	19970369	19970369	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78	11			ENST00000396087.3:c.2457C>T	p.Asp819=	p.D819=	ENST00000396087	NM_001244963.1	819	gaC/gaT	0	0.617	AAGCAGGAGACGCCCCCTCAA
ADAMTS15	170689	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	130332501	130332501	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	129	17			ENST00000299164.2:c.1368C>T	p.Ser456=	p.S456=	ENST00000299164	NM_139055.2	456	tcC/tcT	0	0.647	GCGTGGGCTCCAAGCCCTGTC
PRB3	5544	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	11420209	11420209	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	220	36			ENST00000381842.3:c.847C>T	p.Pro283Ser	p.P283S	ENST00000381842	NM_006249.4	283	Ccc/Tcc	0	0.622	TTTCCAGCGGGAGGTGGCAGA
MGAT4C	25834	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	86374059	86374059	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78	12			ENST00000604798.1:c.445C>T	p.Arg149Cys	p.R149C	ENST00000604798		149	Cgt/Tgt	0	0.398	ATGGCATCACGCCAGGAAGAA
SLC13A2	9058	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	26817446	26817446	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	264	40			ENST00000444914.3:c.353C>T	p.Pro118Leu	p.P118L	ENST00000444914	NM_001145975.1	118	cCg/cTg	0	0.612	GTCTTCCCGCCGCTCAGCCAT
LRRC37B	114659	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	30349672	30349672	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	115	23			ENST00000341671.7:c.1507G>A	p.Val503Met	p.V503M	ENST00000341671	NM_052888.2	503	Gtg/Atg	0	0.507	GGATTCATTGGTGCAGTCTGA
ZNF521	25925	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	18	22805969	22805969	+	missense_variant	Missense_Mutation	SNP	T	T	G			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	147	23			ENST00000361524.3:c.1913A>C	p.Gln638Pro	p.Q638P	ENST00000361524	NM_015461.2	638	cAa/cCa	0	0.478	AGCACCACATTGATTACAGAT
ZNF426	79088	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	9646905	9646905	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74	11			ENST00000535489.1:c.4G>A	p.Ala2Thr	p.A2T	ENST00000535489		2	Gca/Aca	0	0.463	TCAGCAGCTGCCATCCCGCGA
EHD2	30846	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	48229108	48229108	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52	10			ENST00000263277.3:c.542G>A	p.Arg181His	p.R181H	ENST00000263277	NM_014601.3	181	cGc/cAc	0	0.637	TTCGCGGAGCGCGTGGACCTC
KIAA0754	23499	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	39876726	39876726	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29	10			ENST00000530275.1:c.381A>G	p.Thr127=	p.T127=	ENST00000530275	NM_015038.1	127	acA/acG	0	0.512	CGAGGGCCACAAAAAGTTTAG
CEP250	11190	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	20	34059913	34059913	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	186	33			ENST00000397527.1:c.987T>C	p.Ser329=	p.S329=	ENST00000397527	NM_007186.3	329	tcT/tcC	0	0.423	ATGAAGCATCTCTTAGTAGGA
YTHDF1	54915	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	20	61833842	61833842	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82	15			ENST00000370339.3:c.1450G>A	p.Val484Ile	p.V484I	ENST00000370339	NM_017798.3	484	Gta/Ata	0	0.537	TTATTGGGTACATCCTTAACA
VAMP5	10791	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	85818866	85818866	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	102	20			ENST00000306384.4:c.22C>T	p.Arg8Trp	p.R8W	ENST00000306384	NM_006634.2	8	Cgg/Tgg	0	0.602	AGAGTTGGAGCGGTGCCAGCA
AMER3	205147	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	131521800	131521800	+	stop_gained	Nonsense_Mutation	SNP	C	C	T			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45	12			ENST00000423981.1:c.2155C>T	p.Gln719Ter	p.Q719*	ENST00000423981	NM_001105194.1	719	Cag/Tag	0	0.632	CATGCTGGAGCAGAAACAGTC
FN1	2335	hgsc.bcm.edu;ucsc.edu	GRCh37	2	216288193	216288193	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	55	6			ENST00000354785.4:c.1273C>G	p.Leu425Val	p.L425V	ENST00000354785		425	Cta/Gta	0	0.463	TTGTTGTATAGGAAGGGGAAG
RARB	5915	hgsc.bcm.edu;ucsc.edu	GRCh37	3	25470378	25470378	+	splice_region_variant,synonymous_variant	Splice_Region	SNP	A	A	G			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40	6			ENST00000330688.4:c.156A>G	p.Gln52=	p.Q52=	ENST00000330688	NM_000965.3	52	caA/caG	0	0.433	ACACTGCTCAATGTAGGTTTA
CELSR3	1951	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	48678778	48678778	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	125	25			ENST00000164024.4:c.9004C>T	p.Arg3002Trp	p.R3002W	ENST00000164024	NM_001407.2	3002	Cgg/Tgg	0	0.652	CGCTGGGCCCGGCCCAGAGAA
COPB2	9276	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	139085462	139085462	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45	11			ENST00000333188.5:c.1832C>T	p.Pro611Leu	p.P611L	ENST00000333188	NM_004766.2	611	cCt/cTt	0	0.398	TGGAATGGTAGGAAGGACCTT
DNAJB14	79982	hgsc.bcm.edu;ucsc.edu	GRCh37	4	100822294	100822294	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	59	8			ENST00000442697.2:c.1031A>G	p.Tyr344Cys	p.Y344C	ENST00000442697	NM_001278310.1	344	tAt/tGt	0	0.373	TTTTGCTGCATACTGCATATC
ABLIM3	22885	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	148617131	148617131	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	117	29			ENST00000506113.1:c.1009T>C	p.Ser337Pro	p.S337P	ENST00000506113		337	Tcc/Ccc	0	0.522	CAGATACATGTCCGACGAGAT
ATP10B	23120	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	160049524	160049524	+	synonymous_variant	Silent	SNP	G	G	T			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	89	17			ENST00000327245.5:c.1689C>A	p.Thr563=	p.T563=	ENST00000327245	NM_025153.2	563	acC/acA	0	0.488	TGTCTGACAAGGTCTCCAACC
PKHD1	5314	hgsc.bcm.edu;ucsc.edu	GRCh37	6	51897876	51897876	+	missense_variant	Missense_Mutation	SNP	A	A	T			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	56	6			ENST00000371117.3:c.3316T>A	p.Leu1106Ile	p.L1106I	ENST00000371117	NM_138694.3	1106	Tta/Ata	0	0.383	ACTGGATTTAAGGAAGAGACA
MAP7	9053	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	136710581	136710581	+	stop_gained	Nonsense_Mutation	SNP	T	T	A			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	135	25			ENST00000454590.1:c.385A>T	p.Lys129Ter	p.K129*	ENST00000454590	NM_001198614.1	129	Aag/Tag	0	0.542	AACCTCTTCTTCCGCTCTTCC
SYNE1	23345	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	152651648	152651648	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	60	11			ENST00000367255.5:c.14172G>A	p.Ala4724=	p.A4724=	ENST00000367255	NM_182961.3	4724	gcG/gcA	0	0.552	CCCCAAGGCCCGCCACCTCGT
CDK13	8621	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	40102644	40102644	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73	14			ENST00000181839.4:c.2725A>G	p.Thr909Ala	p.T909A	ENST00000181839	NM_031267.3	909	Act/Gct	0	0.333	CGAACTCTTCACTAAAAAACC
POM121L12	285877	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	53103839	53103839	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47	11			ENST00000408890.4:c.475C>T	p.Arg159Cys	p.R159C	ENST00000408890	NM_182595.3	159	Cgc/Tgc	0	0.721	ACAGAGAgcccgccccgcagg
VDAC3	7419	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	42259491	42259491	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57	9			ENST00000521158.1:c.512C>T	p.Ala171Val	p.A171V	ENST00000521158		171	gCc/gTc	0	0.463	AATAATTTCGCCCTGGGTTAC
GSDMD	79792	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	144642132	144642132	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	55	9			ENST00000526406.1:c.403C>T	p.His135Tyr	p.H135Y	ENST00000526406	NM_001166237.1	135	Cat/Tat	0	0.537	GACTCTGCTCCATGAGAGGTG
SLC24A2	25769	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	19786146	19786146	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	86	10			ENST00000341998.2:c.719G>C	p.Arg240Pro	p.R240P	ENST00000341998	NM_001193288.2	240	cGa/cCa	0	0.393	AGACACATCTCGAAAGAGCGG
EXTL1	2134	broad.mit.edu;ucsc.edu	GRCh37	1	26360306	26360306	+	synonymous_variant	Silent	SNP	C	C	T	rs137944707	byFrequency	TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78	17			ENST00000374280.3:c.1638C>T	p.Asn546=	p.N546=	ENST00000374280	NM_004455.2	546	aaC/aaT	0	0.597	AGAGGACCAACGAATTCTCCA
SPRYD3	84926	broad.mit.edu;ucsc.edu	GRCh37	12	53468957	53468957	+	missense_variant	Missense_Mutation	SNP	A	A	C			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	173	27			ENST00000301463.4:c.293T>G	p.Leu98Arg	p.L98R	ENST00000301463	NM_032840.2	98	cTg/cGg	0	0.562	CTGAGGGACCAGCCCCACAGC
LZTR1	8216	broad.mit.edu;ucsc.edu	GRCh37	22	21347144	21347144	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	12	3			ENST00000215739.8:c.1211G>A	p.Gly404Glu	p.G404E	ENST00000215739	NM_006767.3	404	gGg/gAg	0	0.652	TACATCTTCGGGGGCACGGTG
GSDMD	79792	broad.mit.edu;ucsc.edu	GRCh37	8	144645068	144645068	+	synonymous_variant	Silent	SNP	C	C	A			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30	5			ENST00000526406.1:c.1449C>A	p.Pro483=	p.P483=	ENST00000526406	NM_001166237.1	483	ccC/ccA	0	0.667	GCCAGGAGCCCCACTAGCCTG
BMPR1B	658	broad.mit.edu;hgsc.bcm.edu	GRCh37	4	96046194	96046194	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-			TCGA-HW-A5KK-01	TCGA-HW-A5KK-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	50	15			ENST00000440890.2:c.597delC	p.Tyr199Ter	p.Y199*	ENST00000440890		199	taC/ta	0	0.408	ATGAAACTTACATTCCTCCTG
FOLH1	2346	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	49207240	49207240	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33	14			ENST00000256999.2:c.807A>G	p.Thr269=	p.T269=	ENST00000256999	NM_004476.1	269	acA/acG	0	0.428	GGTAACCTGGTGTGAGAGGGT
OR5D14	219436	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	55563532	55563532	+	synonymous_variant	Silent	SNP	G	G	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	191	37			ENST00000335605.1:c.501G>T	p.Arg167=	p.R167=	ENST00000335605	NM_001004735.1	167	cgG/cgT	0	0.502	ATGCTCTCCGGTTAAACTTCT
APOA1	335	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	116707048	116707048	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88	23			ENST00000236850.4:c.280G>A	p.Glu94Lys	p.E94K	ENST00000236850	NM_000039.1	94	Gag/Aag	0	0.592	TCCCAGAACTCCTGGGTCACA
IRAK3	11213	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	66638280	66638280	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	55	18			ENST00000261233.4:c.902T>C	p.Leu301Ser	p.L301S	ENST00000261233	NM_007199.2	301	tTg/tCg	0	0.393	AACATCCTTTTGGATGATCAG
KERA	11081	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	91449807	91449807	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	80	13			ENST00000266719.3:c.252A>G	p.Glu84=	p.E84=	ENST00000266719	NM_007035.3	84	gaA/gaG	0	0.348	CAGGAATGGTTTCTATCAGGT
TMCC3	57458	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	94975589	94975589	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	107	24			ENST00000261226.4:c.804C>T	p.Asn268=	p.N268=	ENST00000261226	NM_020698.2	268	aaC/aaT	0	0.592	ACTGGTTTCCGTTACTGTCGG
ATP8A2	51761	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	13	26411309	26411309	+	synonymous_variant	Silent	SNP	C	C	A			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	121	61			ENST00000381655.2:c.2763C>A	p.Thr921=	p.T921=	ENST00000381655	NM_016529.4	921	acC/acA	0	0.498	AGATTTTCACCGCTTTGCCGC
MYO16	23026	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	13	109318372	109318372	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45	14			ENST00000356711.2:c.101G>A	p.Arg34His	p.R34H	ENST00000356711	NM_015011.1	34	cGc/cAc	0	0.527	TACTATGAGCGCGAGAAGGCT
CASC5	57082	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	40914116	40914116	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	50	10			ENST00000346991.5:c.1732T>C	p.Ser578Pro	p.S578P	ENST00000346991		578	Tca/Cca	0	0.358	GCAGAGCCTGTCAAATCCTTT
TUBGCP4	27229	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	43695930	43695930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149549954	by1000genomes	TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21	23			ENST00000564079.1:c.1781C>T	p.Ser594Leu	p.S594L	ENST00000564079	NM_014444.2	594	tCg/tTg	0	0.527	AGTTTTTGTTCGCTGGTCAGT
AP4E1	23431	hgsc.bcm.edu;broad.mit.edu	GRCh37	15	51260560	51260560	+	missense_variant	Missense_Mutation	SNP	T	T	G			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15	6			ENST00000261842.5:c.1952T>G	p.Leu651Arg	p.L651R	ENST00000261842	NM_001252127.1	651	cTt/cGt	0	0.373	GAGGAAAAGCTTTCTCAGGAA
ACSM1	116285	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	20635526	20635526	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79	22			ENST00000307493.4:c.1539C>T	p.Ala513=	p.A513=	ENST00000307493	NM_052956.2	513	gcC/gcT	0	0.473	GGACAATAAAGGCCTTCACCA
DNAH2	146754	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7643864	7643864	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	129	20			ENST00000572933.1:c.1503C>T	p.Arg501=	p.R501=	ENST00000572933		501	cgC/cgT	0	0.672	TTGCCTCCCGCGAGGTGCGGC
DNAJC7	7266	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	40140910	40140910	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96	51			ENST00000457167.4:c.758C>T	p.Ala253Val	p.A253V	ENST00000457167	NM_003315.3	253	gCc/gTc	0	0.423	GAGTGCTTTGGCATTCTACAG
CSHL1	1444	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	61987091	61987091	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73	42			ENST00000309894.5:c.649G>A	p.Glu217Lys	p.E217K	ENST00000309894	NM_022579.1	217	Gag/Aag	0	0.632	CAGCTGCCCTCCACAGAGCGG
LGALS3BP	3959	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	76967757	76967757	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	55	25			ENST00000262776.3:c.1659G>A	p.Ser553=	p.S553=	ENST00000262776	NM_005567.3	553	tcG/tcA	0	0.612	AGGTGCTCTTCGAGCTGTTGG
LAMA3	3909	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	18	21489195	21489195	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73	13			ENST00000313654.9:c.7094A>G	p.Asn2365Ser	p.N2365S	ENST00000313654	NM_198129.1	2365	aAc/aGc	0	0.453	CCCTTGGGAAACATCTCTGAC
TRAPPC8	22878	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	18	29433858	29433858	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42	10			ENST00000283351.4:c.3387C>G	p.Ser1129Arg	p.S1129R	ENST00000283351	NM_014939.3	1129	agC/agG	0	0.328	TCCAGTGTTTGCTACTACTTG
S1PR2	9294	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	10334891	10334891	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36	15			ENST00000590320.1:c.691C>T	p.Leu231=	p.L231=	ENST00000590320	NM_004230.3	231	Ctg/Ttg	0	0.617	GTCTTGAGCAGGGCTAGCGTC
ZNF585B	92285	hgsc.bcm.edu;broad.mit.edu	GRCh37	19	37676803	37676803	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	109	18			ENST00000532828.2:c.1636G>A	p.Gly546Arg	p.G546R	ENST00000532828	NM_152279.3	546	Gga/Aga	0	0.383	TGTCTCTCTCCAGTGTGAATT
FCGBP	8857	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	40368357	40368357	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	293	32			ENST00000221347.6:c.12991G>A	p.Ala4331Thr	p.A4331T	ENST00000221347	NM_003890.2	4331	Gcc/Acc	0	0.647	GCCTGGCAGGCGGCCACGTAG
AJAP1	55966	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	4832380	4832380	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69	11			ENST00000378191.4:c.958C>T	p.Arg320Trp	p.R320W	ENST00000378191	NM_018836.3	320	Cgg/Tgg	0	0.607	CAGCCACCAGCGGAAGACCAA
CLSTN1	22883	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	9794036	9794036	+	missense_variant	Missense_Mutation	SNP	A	A	C			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97	19			ENST00000377298.4:c.2275T>G	p.Phe759Val	p.F759V	ENST00000377298	NM_001009566.1	759	Ttc/Gtc	0	0.612	TTACCTGTGAAGGTCATGCCC
SPRR2G	6706	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	153122438	153122438	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	120	23			ENST00000368748.4:c.149C>T	p.Pro50Leu	p.P50L	ENST00000368748	NM_001014291.3	50	cCa/cTa	0	0.567	ATCCTGGCATGGTGGAGGTGG
CD244	51744	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	160811431	160811431	+	stop_gained	Nonsense_Mutation	SNP	C	C	A			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	102	26			ENST00000368033.3:c.322G>T	p.Glu108Ter	p.E108*	ENST00000368033		108	Gag/Tag	0	0.453	CTGGTGACCTCCAGGCAGTAG
RXRG	6258	hgsc.bcm.edu;broad.mit.edu	GRCh37	1	165398112	165398112	+	missense_variant	Missense_Mutation	SNP	A	A	C			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	66	5			ENST00000359842.5:c.141T>G	p.Asp47Glu	p.D47E	ENST00000359842	NM_001256570.1	47	gaT/gaG	0	0.607	TCACTGGGGTATCTGTGTAGC
SELE	6401	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	169697059	169697059	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	137	34			ENST00000333360.7:c.1289G>A	p.Cys430Tyr	p.C430Y	ENST00000333360	NM_000450.2	430	tGc/tAc	0	0.498	GACAGCATCGCATCTCACAGC
EDEM3	80267	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	184695449	184695449	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61	15			ENST00000318130.8:c.687A>G	p.Ala229=	p.A229=	ENST00000318130	NM_025191.3	229	gcA/gcG	0	0.388	TCAAGGTACCTGCACAAGCTG
GPR137B	7107	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	236341829	236341829	+	stop_gained	Nonsense_Mutation	SNP	C	C	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	180	58			ENST00000366592.3:c.580C>T	p.Arg194Ter	p.R194*	ENST00000366592	NM_003272.3	194	Cga/Tga	0	0.478	CGTCTCTGTGCGAGTGGCCAT
RYR2	6262	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	237804239	237804239	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	50	8			ENST00000366574.2:c.7158C>G	p.Asn2386Lys	p.N2386K	ENST00000366574	NM_001035.2	2386	aaC/aaG	0	0.443	ACATGGGGAACGCGATCATGA
BCL11A	53335	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	60679728	60679728	+	downstream_gene_variant	3'Flank	SNP	C	C	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	119	38						ENST00000335712	NM_022893.3			0	0.557	TAAGGGCTCTCGAGCTTCCAT
RND3	390	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	151326607	151326607	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	125	34			ENST00000375734.2:c.629C>T	p.Ser210Leu	p.S210L	ENST00000375734	NM_001254738.1	210	tCa/tTa	0	0.458	GGCTCTCTGTGATTTGTTCCG
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74	18			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
BSN	8927	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	49691512	49691512	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	72	11			ENST00000296452.4:c.4523C>T	p.Thr1508Met	p.T1508M	ENST00000296452	NM_003458.3	1508	aCg/aTg	0	0.622	TCTACACAGACGCCAAGTCCA
BSN	8927	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	49694614	49694614	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41	14			ENST00000296452.4:c.7625C>T	p.Thr2542Met	p.T2542M	ENST00000296452	NM_003458.3	2542	aCg/aTg	0	0.632	TCACTGCAAACGGAGGAGCAG
CACNA2D3	55799	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	54596855	54596855	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40	10			ENST00000474759.1:c.573G>T	p.Trp191Cys	p.W191C	ENST00000474759	NM_018398.2	191	tgG/tgT	0	0.403	GGGTTTATTGGTCTGAATCTC
SEL1L3	23231	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	25849135	25849135	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73	9			ENST00000399878.3:c.514A>G	p.Ile172Val	p.I172V	ENST00000399878	NM_015187.3	172	Ata/Gta	0	0.408	GCGCGTACTATCACTGCAGAT
SHROOM3	57619	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	77661578	77661578	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33	5			ENST00000296043.6:c.2252C>T	p.Pro751Leu	p.P751L	ENST00000296043	NM_020859.3	751	cCg/cTg	0	0.692	CCCTCGCACCCGCACACATCC
FRAS1	80144	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	79400621	79400621	+	missense_variant	Missense_Mutation	SNP	T	T	G			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41	15			ENST00000264895.6:c.8192T>G	p.Phe2731Cys	p.F2731C	ENST00000264895	NM_025074.6	2731	tTt/tGt	0	0.463	GGCTCTGATTTTAAATCTAGA
USP53	54532	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	120214081	120214081	+	missense_variant	Missense_Mutation	SNP	T	T	A			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	50	9			ENST00000450251.1:c.2937T>A	p.Asp979Glu	p.D979E	ENST00000450251		979	gaT/gaA	0	0.393	ATATGAATGATGAAAGACATA
PRDM5	11107	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	121698363	121698363	+	missense_variant	Missense_Mutation	SNP	A	A	C			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	155	35			ENST00000264808.3:c.1517T>G	p.Val506Gly	p.V506G	ENST00000264808	NM_018699.2	506	gTt/gGt	0	0.383	CCGGATATGAACTCTGAGTGT
GMDS	2762	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	1726688	1726688	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	194	37			ENST00000380815.4:c.949G>A	p.Val317Met	p.V317M	ENST00000380815	NM_001500.3	317	Gtg/Atg	0	0.507	TCCACAGTCACGTGAACTTTG
GPR116	221395	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	46826760	46826760	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	114	16			ENST00000283296.7:c.2880G>A	p.Arg960=	p.R960=	ENST00000283296	NM_001098518.1	960	agG/agA	0	0.478	TGTTGGCAAGCCTGAAGTTCC
NT5E	4907	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	86203685	86203685	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	103	14			ENST00000257770.3:c.1688T>C	p.Leu563Pro	p.L563P	ENST00000257770	NM_002526.3	563	cTt/cCt	0	0.353	TTAATATTTCTTTCACTTTGG
RNGTT	8732	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	89563379	89563379	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	108	13			ENST00000369485.4:c.1001G>A	p.Arg334His	p.R334H	ENST00000369485	NM_003800.3	334	cGt/cAt	0	0.289	TAAATGCATACGAAGATCTTT
TMEM200A	114801	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	130761742	130761742	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93	61			ENST00000392429.1:c.175T>C	p.Ser59Pro	p.S59P	ENST00000392429	NM_052913.2	59	Tcc/Ccc	0	0.478	CCGGCTTTATTCCCCATCTGG
FOXP2	93986	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	114282537	114282537	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61	35			ENST00000408937.3:c.923G>A	p.Gly308Asp	p.G308D	ENST00000408937	NM_014491.3	308	gGc/gAc	0	0.428	GAAGACAATGGCATTAAACAT
WNT2	7472	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	116960776	116960776	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37	10			ENST00000265441.3:c.155G>A	p.Arg52Gln	p.R52Q	ENST00000265441	NM_003391.2	52	cGg/cAg	0	0.597	ACACAGCTGCCGCTGGCTGCT
AKR1B10	57016	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	134212705	134212705	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97	19			ENST00000359579.4:c.42C>T	p.Pro14=	p.P14=	ENST00000359579	NM_020299.4	14	ccC/ccT	0	0.502	CCAAGATGCCCATTGTGGGCC
POLR3D	661	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	22107627	22107627	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	59	36			ENST00000397802.4:c.961C>A	p.Leu321Met	p.L321M	ENST00000397802		321	Ctg/Atg	0	0.542	CCTGGCTGACCTGACAGAGGG
DOCK5	80005	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	25154057	25154057	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	20	4			ENST00000276440.7:c.499G>C	p.Asp167His	p.D167H	ENST00000276440	NM_024940.6	167	Gat/Cat	0	0.512	GGTGGTGCGAGATGACAATGG
NRG1	3084	hgsc.bcm.edu;ucsc.edu	GRCh37	8	32600199	32600199	+	synonymous_variant	Silent	SNP	A	A	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	205	39			ENST00000356819.4:c.639A>T	p.Pro213=	p.P213=	ENST00000356819	NM_013956.3	213	ccA/ccT	0	0.423	TCAGGTGCCCAAATGAGTTTA
ANK1	286	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	41543690	41543690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138642972	byFrequency	TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	81	29			ENST00000265709.8:c.4493G>A	p.Arg1498His	p.R1498H	ENST00000265709	NM_001142446.1	1498	cGt/cAt	0	0.522	TTGGCCTTCACGGATGACCCA
CLVS1	157807	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	62371030	62371030	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	55	24			ENST00000519846.1:c.906C>T	p.Ser302=	p.S302=	ENST00000519846		302	tcC/tcT	0	0.502	CTCACACATCCTATAATGCAA
COL5A1	1289	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	137591840	137591840	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	131	29			ENST00000371817.3:c.363C>T	p.Asn121=	p.N121=	ENST00000371817	NM_001278074.1	121	aaC/aaT	0	0.587	CCATCTACAACGAGCAGGGTA
GYG2	8908	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	2799186	2799186	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	32	7			ENST00000381163.3:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000381163	NM_001079855.1	480	Cgt/Tgt	0	0.572	GGAGGAAGGCCGTATCGACTA
PRPS2	5634	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	12838861	12838861	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76	19			ENST00000398491.2:c.812C>T	p.Ala271Val	p.A271V	ENST00000398491		271	gCt/gTt	0	0.483	GCCTTTGAGGCTGTTGTCGTC
RS1	6247	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	18660177	18660177	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	70	28			ENST00000379984.3:c.622G>A	p.Val208Ile	p.V208I	ENST00000379984	NM_000330.3	208	Gtc/Atc	0	0.657	GCAATGCGGACGTGCCAGCCC
POLA1	5422	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	24830876	24830876	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	50	24			ENST00000379059.3:c.3174G>A	p.Leu1058=	p.L1058=	ENST00000379059	NM_016937.3	1058	ctG/ctA	0	0.393	ACGCTGCTCTGGTTGTTGAGC
FAM47B	170062	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	34962025	34962025	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	60	21			ENST00000329357.5:c.1077C>T	p.Asp359=	p.D359=	ENST00000329357	NM_152631.2	359	gaC/gaT	0	0.537	AGCTGGAAGACGCACGGGCTC
FAM120C	54954	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	54209051	54209051	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17	7			ENST00000375180.2:c.581C>T	p.Ala194Val	p.A194V	ENST00000375180	NM_017848.4	194	gCg/gTg	0	0.721	GATCAGTTGCGCTGTCTGCCG
USP51	158880	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	55514135	55514135	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	48	15			ENST00000500968.3:c.1238C>T	p.Ser413Leu	p.S413L	ENST00000500968	NM_201286.3	413	tCg/tTg	0	0.438	ATGAAAAAGCGAAGACATTTC
KIAA2022	340533	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	73963361	73963361	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	72	17			ENST00000055682.6:c.1031C>A	p.Thr344Asn	p.T344N	ENST00000055682	NM_001008537.2	344	aCc/aAc	0	0.463	CTTGGGGCAGGTAGTAAAGAC
AMMECR1	9949	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	109459855	109459855	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	101	21			ENST00000262844.5:c.590T>C	p.Leu197Pro	p.L197P	ENST00000262844	NM_015365.2	197	cTt/cCt	0	0.378	GCTATCTTTAAGGGCACTGTT
CFP	5199	broad.mit.edu;ucsc.edu	GRCh37	X	47487019	47487019	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17	7			ENST00000247153.3:c.425G>T	p.Trp142Leu	p.W142L	ENST00000247153	NM_002621.2	142	tGg/tTg	0	0.632	CCAGGGCCCCCAGCCAGACCA
OBSCN	84033	broad.mit.edu;ucsc.edu	GRCh37	1	228404888	228404888	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	113	15			ENST00000570156.2:c.2552C>T	p.Thr851Met	p.T851M	ENST00000570156	NM_001271223.2	851	aCg/aTg	0	0.652	GATGTGGGGACGCGGCACCGG
ZDBF2	57683	broad.mit.edu;ucsc.edu	GRCh37	2	207169761	207169761	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37	9			ENST00000374423.3:c.509C>T	p.Ala170Val	p.A170V	ENST00000374423	NM_020923.1	170	gCt/gTt	0	0.423	ATTGGTCAGGCTACAAATAAT
SP100	6672	broad.mit.edu;ucsc.edu	GRCh37	2	231367785	231367785	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	92	18			ENST00000340126.4:c.1725A>G	p.Arg575=	p.R575=	ENST00000340126	NM_001080391.1	575	agA/agG	0	0.289	TCTCAGGAAGAAAAGCCAACA
SERPINB11	89778	broad.mit.edu;ucsc.edu	GRCh37	18	61387343	61387343	+	missense_variant	Missense_Mutation	SNP	A	A	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33	8			ENST00000544088.1:c.572A>T	p.Lys191Ile	p.K191I	ENST00000544088	NM_080475.2	191	aAa/aTa	0	0.348	TGGCAAAATAAATTTCAAGTA
SELENOF	9403	broad.mit.edu;ucsc.edu	GRCh37	1	87369113	87369113	+	stop_gained	Nonsense_Mutation	SNP	C	C	A			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	20	12			ENST00000331835.5:c.94G>T	p.Glu32Ter	p.E32*	ENST00000331835	NM_004261.3	32	Gag/Tag	0	0.418	GATGAAAACTCTGCCCCAAAA
OR9G1	390174	broad.mit.edu;ucsc.edu	GRCh37	11	56468417	56468417	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	130	29			ENST00000312153.1:c.554A>G	p.Glu185Gly	p.E185G	ENST00000312153	NM_001005213.1	185	gAg/gGg	0	0.463	CCCTTGGTGGAGCTGGCCTGT
ADAMTS18	170692	broad.mit.edu;ucsc.edu	GRCh37	16	77401350	77401350	+	stop_gained	Nonsense_Mutation	SNP	G	G	A			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78	20			ENST00000282849.5:c.766C>T	p.Arg256Ter	p.R256*	ENST00000282849	NM_199355.2	256	Cga/Tga	0	0.443	TTCTTGCGTCGTCCACAAAAA
PCSK2	5126	broad.mit.edu;ucsc.edu	GRCh37	20	17446133	17446133	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	48	6			ENST00000262545.2:c.1365G>T	p.Met455Ile	p.M455I	ENST00000262545	NM_002594.3	455	atG/atT	0	0.567	TGGTGAAAATGGCTAAAGACT
CISH	1154	broad.mit.edu;ucsc.edu	GRCh37	3	50645154	50645154	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	104	23			ENST00000443053.2:c.712C>T	p.Arg238Cys	p.R238C	ENST00000443053	NM_013324.5	238	Cgc/Tgc	0	0.622	TGCAGGCTGCGGGCACTGCTT
HTR1E	3354	broad.mit.edu;ucsc.edu	GRCh37	6	87725427	87725427	+	synonymous_variant	Silent	SNP	C	C	A			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	129	18			ENST00000305344.5:c.375C>A	p.Thr125=	p.T125=	ENST00000305344	NM_000865.2	125	acC/acA	0	0.562	GGGCCATCACCAATGCTATTG
TNXB	7148	broad.mit.edu;ucsc.edu	GRCh37	6	32049264	32049264	+	upstream_gene_variant	5'Flank	SNP	G	G	A			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	19	4						ENST00000516703				0	0.617	CTCATCCCCCGCAACAGGCAC
TP53	7157	broad.mit.edu;hgsc.bcm.edu	GRCh37	17	7577105	7577105	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	13	38			ENST00000269305.4:c.833delC	p.Pro278LeufsTer67	p.P278Lfs*67	ENST00000269305	NM_001126112.2	278	cCt/ct	0	0.552	GTCTCTCCCAGGACAGGCACA
EMILIN2	84034	broad.mit.edu;hgsc.bcm.edu	GRCh37	18	2891806	2891806	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62	23			ENST00000254528.3:c.1682delC	p.Pro561LeufsTer23	p.P561Lfs*23	ENST00000254528	NM_032048.2	561	Cct/ct	0	0.502	CCAGGGAAAGCCTCATGGGAT
CYTH4	27128	broad.mit.edu;hgsc.bcm.edu	GRCh37	22	37705324	37705326	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-			TCGA-CS-6665-01	TCGA-CS-6665-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	80	45			ENST00000248901.6:c.772_774delTTC	p.Phe258del	p.F258del	ENST00000248901	NM_013385.3	256	acCTTc/acc	0	0.567	TCACTCACACCTTCTTCAATCCA
AK7	122481	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	14	96944967	96944967	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7686-01	TCGA-HT-7686-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	60	43			ENST00000267584.4:c.1721T>C	p.Phe574Ser	p.F574S	ENST00000267584	NM_152327.3	574	tTt/tCt	0	0.478	TTCAACTATTTTGATGAACTT
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	by1000genomes	TCGA-HT-7686-01	TCGA-HT-7686-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4	14			ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	0	0.542	GGCACAAACACGCACCTCAAA
MYH2	4620	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	10429940	10429940	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7686-01	TCGA-HT-7686-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	195	61			ENST00000245503.5:c.4163G>A	p.Arg1388His	p.R1388H	ENST00000245503	NM_017534.5	1388	cGc/cAc	0	0.512	CTCCTCTGTGCGCTGGATGGC
TUBG1	7283	hgsc.bcm.edu;broad.mit.edu	GRCh37	17	40767042	40767042	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7686-01	TCGA-HT-7686-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42	4			ENST00000251413.3:c.1339G>A	p.Gly447Ser	p.G447S	ENST00000251413	NM_001070.4	447	Ggc/Agc	0	0.582	CATCTCCTGGGGCACCCAGGA
PRDM16	63976	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	3342279	3342279	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7686-01	TCGA-HT-7686-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	156	16			ENST00000270722.5:c.3074G>A	p.Arg1025Gln	p.R1025Q	ENST00000270722		1025	cGg/cAg	0	0.662	AACCTGGACCGGCACCTCAAG
SLC16A4	9122	hgsc.bcm.edu;ucsc.edu	GRCh37	1	110921952	110921952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35157487	byFrequency	TCGA-HT-7686-01	TCGA-HT-7686-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45	16			ENST00000369779.4:c.553G>A	p.Ala185Thr	p.A185T	ENST00000369779	NM_001201547.1	185	Gca/Aca	0	0.378	AAATTCAATGCGATAGCTCCA
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HT-7686-01	TCGA-HT-7686-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	63	38			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
PLCH1	23007	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	155200712	155200712	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7686-01	TCGA-HT-7686-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69	41			ENST00000340059.7:c.3127A>G	p.Ile1043Val	p.I1043V	ENST00000340059	NM_001130960.1	1043	Att/Gtt	0	0.458	GTAGATACAATGGTGTCCCCT
ANXA10	11199	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	169105805	169105805	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-HT-7686-01	TCGA-HT-7686-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96	57			ENST00000359299.3:c.879T>C	p.Tyr293=	p.Y293=	ENST00000359299	NM_007193.4	293	taT/taC	0	0.353	AAGAGCGATATGGAAAATCCC
PRDM9	56979	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	23526872	23526872	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7686-01	TCGA-HT-7686-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	92	31			ENST00000296682.3:c.1675C>T	p.Arg559Trp	p.R559W	ENST00000296682	NM_020227.2	559	Cgg/Tgg	0	0.527	GGAGTGTGGGCGGGGCTTTAG
HCN1	348980	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	45262356	45262356	+	synonymous_variant	Silent	SNP	G	G	T			TCGA-HT-7686-01	TCGA-HT-7686-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42	21			ENST00000303230.4:c.2340C>A	p.Thr780=	p.T780=	ENST00000303230	NM_021072.3	780	acC/acA	0	0.632	TGACTTCCCGGGTCAGGTTGG
DHX29	54505	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	54577281	54577281	+	synonymous_variant	Silent	SNP	G	G	C			TCGA-HT-7686-01	TCGA-HT-7686-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	65	40			ENST00000251636.5:c.2028C>G	p.Leu676=	p.L676=	ENST00000251636	NM_019030.2	676	ctC/ctG	0	0.393	TTGTACAATAGAGTAACCTGG
UNC5CL	222643	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	40996311	40996311	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-HT-7686-01	TCGA-HT-7686-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79	34			ENST00000244565.3:c.1358C>A	p.Pro453His	p.P453H	ENST00000244565	NM_173561.2	453	cCc/cAc	0	0.672	GGCCGCTGCGGGGCTGCGCTG
ADAM28	10863	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	24201057	24201057	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-HT-7686-01	TCGA-HT-7686-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	66	34			ENST00000265769.4:c.1950A>G	p.Gly650=	p.G650=	ENST00000265769	NM_014265.4	650	ggA/ggG	0	0.498	GTGAGGAAGGATGGATCCCTC
PKHD1L1	93035	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	110408325	110408325	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7686-01	TCGA-HT-7686-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	16	12			ENST00000378402.5:c.881T>C	p.Phe294Ser	p.F294S	ENST00000378402	NM_177531.4	294	tTc/tCc	0	0.403	AGTGGGCGTTTCTTTGATCAG
EPPK1	83481	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	144941387	144941387	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-HT-7686-01	TCGA-HT-7686-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	22	15			ENST00000525985.1:c.6035C>A	p.Ala2012Asp	p.A2012D	ENST00000525985	NM_031308.2	2012	gCc/gAc	0	0.627	ACCCCCCGTGGCCACCTGCAC
CCNB3	85417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	50055581	50055581	+	missense_variant	Missense_Mutation	SNP	T	T	A			TCGA-HT-7686-01	TCGA-HT-7686-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	156	23			ENST00000376042.1:c.3372T>A	p.Ser1124Arg	p.S1124R	ENST00000376042		1124	agT/agA	0	0.383	GTGATCCAAGTTTCAACCCAA
UBAP1	51271	broad.mit.edu;ucsc.edu	GRCh37	9	34250662	34250662	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-HT-7686-01	TCGA-HT-7686-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35	19			ENST00000545103.1:c.1465G>T	p.Asp489Tyr	p.D489Y	ENST00000545103	NM_001171201.1	489	Gac/Tac	0	0.468	TTAGATTCTCGACTATCTCTT
ATRX	546	broad.mit.edu;hgsc.bcm.edu	GRCh37	X	76920224	76920224	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-			TCGA-HT-7686-01	TCGA-HT-7686-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	50	13			ENST00000373344.5:c.3853delT	p.Ser1285ProfsTer61	p.S1285Pfs*61	ENST00000373344	NM_000489.3	1285	Tcc/cc	0	0.373	TCATCAGAGGAAAGATTGGCT
MPP7	143098	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	28345529	28345529	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	49	50			ENST00000337532.5:c.1431A>G	p.Leu477=	p.L477=	ENST00000337532	NM_173496.3	477	ctA/ctG	0	0.333	GCTTAAATTCTAGTGTCCTTA
OR52I2	143502	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	4608789	4608789	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	46	64			ENST00000312614.4:c.747C>G	p.Ile249Met	p.I249M	ENST00000312614	NM_001005170.2	249	atC/atG	0	0.488	CCTCCTATATCTTAATTCTCA
OR51L1	119682	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	5021019	5021019	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	34	5			ENST00000321543.1:c.807T>C	p.His269=	p.H269=	ENST00000321543	NM_001004755.1	269	caT/caC	0	0.463	TTGGGAAGCATCTGTCTCCCA
MRGPRX3	117195	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	18159642	18159642	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11	28			ENST00000396275.2:c.893C>T	p.Thr298Met	p.T298M	ENST00000396275	NM_054031.3	298	aCg/aTg	0	0.562	CTGCAGGACACGCCTGAGGTG
OR9G4	283189	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	56510829	56510829	+	synonymous_variant	Silent	SNP	G	G	A	rs149257582		TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	191	15			ENST00000302957.3:c.459C>T	p.Thr153=	p.T153=	ENST00000302957	NM_001005284.1	153	acC/acT	0	0.478	TACAGAGGGCGGTGGACATGG
PTGR2	145482	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	14	74347933	74347933	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	66	51			ENST00000555661.1:c.877A>G	p.Lys293Glu	p.K293E	ENST00000555661		293	Aaa/Gaa	0	0.358	ATTAAATTATAAAGACAAATT
ISLR	3671	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	74467824	74467824	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52	14			ENST00000249842.3:c.625G>A	p.Ala209Thr	p.A209T	ENST00000249842	NM_005545.3	209	Gcc/Acc	0	0.652	GGACAACATCGCCTGCACCTC
CRAMP1L	57585	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	1706072	1706072	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	16	10			ENST00000397412.3:c.1314C>T	p.Asp438=	p.D438=	ENST00000397412		438	gaC/gaT	0	0.706	GTGCCAAGGACGCCCACGTGC
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652		TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41	26			ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	0	0.572	GATGGGCCTCCGGTTCATGCC
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A			TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	22	25			ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	0	0.552	CCTTCCACTCGGATAAGATGC
ZC3H4	23211	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	47570840	47570840	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	19	13			ENST00000253048.5:c.2685C>T	p.Ala895=	p.A895=	ENST00000253048	NM_015168.1	895	gcC/gcT	0	0.701	AGGTGGGCAGGGCGCGAGCCA
HIVEP3	59269	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	41978828	41978828	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39	31			ENST00000372583.1:c.6064G>A	p.Gly2022Ser	p.G2022S	ENST00000372583	NM_024503.4	2022	Ggc/Agc	0	0.632	GGGAGAGCGCCCATGCCCCTT
CD1E	913	hgsc.bcm.edu;ucsc.edu	GRCh37	1	158325319	158325319	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33	4			ENST00000368167.3:c.585G>A	p.Ala195=	p.A195=	ENST00000368167	NM_030893.3	195	gcG/gcA	0	0.478	GATTTCTAGCGGGGCTCATGG
OR2T1	26696	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	248570030	248570030	+	synonymous_variant	Silent	SNP	C	C	T	rs148427102		TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	49	36			ENST00000366474.1:c.735C>T	p.Tyr245=	p.Y245=	ENST00000366474	NM_030904.1	245	taC/taT	0	0.493	CAGCCCTCTACGAGACAGTGA
MYH7B	57644	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	20	33581234	33581234	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	19	14			ENST00000262873.7:c.2531G>A	p.Arg844His	p.R844H	ENST00000262873	NM_020884.3	844	cGc/cAc	0	0.672	AGCCGTGGCCGCCTCATGCGC
DGCR2	9993	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	22	19026633	19026633	+	splice_region_variant,synonymous_variant	Splice_Region	SNP	G	G	A	rs146027196		TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33	14			ENST00000263196.7:c.1398C>T	p.Asp466=	p.D466=	ENST00000263196	NM_001184781.1	466	gaC/gaT	0	0.622	AAGCATCATCGTCTGCAGGAA
APOB	338	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	21226157	21226157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149273387		TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	242	122			ENST00000233242.1:c.12137G>A	p.Arg4046Gln	p.R4046Q	ENST00000233242	NM_000384.2	4046	cGg/cAg	0	0.408	ATCAGATTCCCGGACCCTCAA
SCN2A	6326	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	166211024	166211024	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52	30			ENST00000357398.3:c.3242G>C	p.Ser1081Thr	p.S1081T	ENST00000357398		1081	aGt/aCt	0	0.388	ATAGGCAGCAGTGTAGAAAAA
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	50	28			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
ANKRD28	23243	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	15719776	15719776	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17	17			ENST00000399451.2:c.2557G>A	p.Asp853Asn	p.D853N	ENST00000399451	NM_015199.3	853	Gac/Aac	0	0.398	CCTGTAGAGTCCACAGAATTG
SATB1	6304	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	18435971	18435971	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	104	47			ENST00000417717.2:c.1189G>T	p.Ala397Ser	p.A397S	ENST00000417717	NM_001195470.1	397	Gct/Tct	0	0.433	CTGTTAAAAGCCACACGTGCA
SLC4A7	9497	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	27439832	27439832	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	48	50			ENST00000295736.5:c.2413C>G	p.Leu805Val	p.L805V	ENST00000295736	NM_003615.4	805	Ctt/Gtt	0	0.363	ACACCACGAAGTTTTTTACAT
MYH15	22989	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	108195254	108195254	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26	28			ENST00000273353.3:c.1283C>T	p.Thr428Ile	p.T428I	ENST00000273353	NM_014981.1	428	aCt/aTt	0	0.338	CTGTTCTATAGTTTGACCTCT
HCN1	348980	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	45262407	45262407	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35	33			ENST00000303230.4:c.2289G>A	p.Pro763=	p.P763=	ENST00000303230	NM_021072.3	763	ccG/ccA	0	0.652	CTTCATTTTTCGGCGTGGAGC
ERAP2	64167	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	96215430	96215430	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	92	8			ENST00000437043.3:c.41C>T	p.Pro14Leu	p.P14L	ENST00000437043	NM_001130140.1	14	cCa/cTa	0	0.373	CACAGAAAACCAATGTTTAAC
LIMK1	3984	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	73511062	73511062	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40	18			ENST00000336180.2:c.263C>G	p.Ser88Cys	p.S88C	ENST00000336180	NM_002314.3	88	tCt/tGt	0	0.597	CATGGGTGCTCTGAGCAAATC
LRRCC1	85444	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	86021973	86021973	+	missense_variant	Missense_Mutation	SNP	T	T	G			TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	12	9			ENST00000360375.3:c.248T>G	p.Leu83Arg	p.L83R	ENST00000360375	NM_033402.4	83	cTa/cGa	0	0.323	ATTGAAGGACTAAACACACTG
RASEF	158158	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	85607825	85607825	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184	82			ENST00000376447.3:c.2036C>G	p.Ala679Gly	p.A679G	ENST00000376447	NM_152573.3	679	gCc/gGc	0	0.473	TCTTACCATGGCCAGTTTCTC
ZNF189	7743	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	104170609	104170609	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	112	37			ENST00000339664.2:c.559C>T	p.Arg187Cys	p.R187C	ENST00000339664	NM_001278240.1	187	Cgc/Tgc	0	0.413	AAGTTTTAGTCGCAGTTCATT
CAMSAP1	157922	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	138713009	138713009	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	112	107			ENST00000389532.4:c.3498C>T	p.Phe1166=	p.F1166=	ENST00000389532	NM_015447.3	1166	ttC/ttT	0	0.567	TGTAACTGTCGAAGAGACACT
PBDC1	51260	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	75396760	75396760	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88	34			ENST00000373358.3:c.342C>G	p.Asp114Glu	p.D114E	ENST00000373358	NM_016500.3	114	gaC/gaG	0	0.423	TTGTTGAAGACTTCAACTATG
ATRX	546	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	76940431	76940431	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T			TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71	36			ENST00000373344.5:c.662G>A	p.Arg221Lys	p.R221K	ENST00000373344	NM_000489.3	221	aGg/aAg	0	0.328	TATTACCTACCTACATTGTTC
PLS3	5358	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	114882253	114882253	+	missense_variant	Missense_Mutation	SNP	T	T	G			TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	108	66			ENST00000420625.2:c.1676T>G	p.Ile559Ser	p.I559S	ENST00000420625	NM_001136025.3	559	aTt/aGt	0	0.403	GTGGATTTAATTGATGCCATC
ZNF275	10838	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	152612569	152612569	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	19	19			ENST00000370251.3:c.426G>A	p.Ala142=	p.A142=	ENST00000370251	NM_001080485.3	142	gcG/gcA	0	0.607	GGGGGGTGGCGGAGTTTAATG
CANT1	124583	broad.mit.edu;ucsc.edu	GRCh37	17	76991172	76991172	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3	3			ENST00000302345.2:c.763G>A	p.Gly255Ser	p.G255S	ENST00000302345	NM_001159773.1	255	Ggc/Agc	0	0.652	TCCACGCTGCCCTTGTAGCCC
AKAP5	9495	broad.mit.edu;hgsc.bcm.edu	GRCh37	14	64936370	64936374	+	frameshift_variant	Frame_Shift_Del	DEL	AATAA	AATAA	-			TCGA-HW-8319-01	TCGA-HW-8319-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	86	21			ENST00000394718.4:c.1264_1268delATAAA	p.Ile422GlnfsTer18	p.I422Qfs*18	ENST00000394718	NM_004857.3	420	AATAAa/a	0	0.341	CTCTGATGATAATAAAATAAACAAT
FAM186B	84070	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	49992644	49992644	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs140386687	byFrequency	TCGA-DB-5280-01	TCGA-DB-5280-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79	66			ENST00000257894.2:c.2258T>C	p.Ile753Thr	p.I753T	ENST00000257894	NM_032130.2	753	aTt/aCt	0	0.537	CAGGCGGTCAATGTTTTCCAG
VRK1	7443	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	14	97321577	97321577	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-DB-5280-01	TCGA-DB-5280-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	106	78			ENST00000216639.3:c.593A>G	p.Tyr198Cys	p.Y198C	ENST00000216639	NM_003384.2	198	tAt/tGt	0	0.393	TTGGTAGATTATGGCCTTGCT
TNFAIP2	7127	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	14	103599762	103599762	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DB-5280-01	TCGA-DB-5280-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	59	43			ENST00000560869.1:c.1609C>T	p.Arg537Cys	p.R537C	ENST00000560869		537	Cgc/Tgc	0	0.622	CAGCAAGGGGCGCCTGGTCCT
TAT	6898	hgsc.bcm.edu;broad.mit.edu	GRCh37	16	71602180	71602180	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-DB-5280-01	TCGA-DB-5280-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	63	3			ENST00000355962.4:c.1232A>G	p.Glu411Gly	p.E411G	ENST00000355962	NM_000353.2	411	gAg/gGg	0	0.502	ATTCGGGTACTCAAAGCACTG
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	by1000genomes	TCGA-DB-5280-01	TCGA-DB-5280-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	31	30			ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	0	0.542	GGCACAAACACGCACCTCAAA
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7578466	7578466	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-DB-5280-01	TCGA-DB-5280-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47	49			ENST00000269305.4:c.464C>A	p.Thr155Asn	p.T155N	ENST00000269305	NM_001126112.2	155	aCc/aAc	0	0.612	GCGGACGCGGGTGCCGGGCGG
DSG4	147409	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	18	28983444	28983444	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DB-5280-01	TCGA-DB-5280-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	34	28			ENST00000359747.4:c.1483C>T	p.Pro495Ser	p.P495S	ENST00000359747	NM_001134453.1	495	Cca/Tca	0	0.383	TGATTATTGTCCAAACATTTT
NUMBL	9253	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	41183289	41183289	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-DB-5280-01	TCGA-DB-5280-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	27	18			ENST00000252891.4:c.578C>G	p.Ala193Gly	p.A193G	ENST00000252891	NM_004756.3	193	gCc/gGc	0	0.697	CAGGCAGGCGGCAAAAGCACA
ITPKC	80271	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	41223412	41223412	+	synonymous_variant	Silent	SNP	A	A	C			TCGA-DB-5280-01	TCGA-DB-5280-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	80	42			ENST00000263370.2:c.372A>C	p.Leu124=	p.L124=	ENST00000263370	NM_025194.2	124	ctA/ctC	0	0.607	GGACGCATCTAGAATGGAGCT
LILRA2	11027	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	55086405	55086405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs74454618		TCGA-DB-5280-01	TCGA-DB-5280-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	109	99			ENST00000251377.3:c.560C>T	p.Pro187Leu	p.P187L	ENST00000251377		187	cCg/cTg	0	0.587	CCCGTGAGCCCGAGTCGCAGG
MYOM3	127294	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	24419503	24419503	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DB-5280-01	TCGA-DB-5280-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	20	19			ENST00000374434.3:c.1024C>T	p.Leu342Phe	p.L342F	ENST00000374434	NM_152372.3	342	Ctc/Ttc	0	0.637	ACCATGTAGAGCCCCTCGTCC
ZCCHC11	23318	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	52889613	52889613	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-DB-5280-01	TCGA-DB-5280-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	19	16			ENST00000257177.4:c.4932G>A	p.Ser1644=	p.S1644=	ENST00000257177		1644	tcG/tcA	0	0.507	CGCATTACTCCGACACGTTTC
FCRL3	115352	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	157665373	157665373	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-DB-5280-01	TCGA-DB-5280-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47	24			ENST00000368184.3:c.1157C>A	p.Thr386Asn	p.T386N	ENST00000368184	NM_052939.3	386	aCc/aAc	0	0.557	AGCCCTGAAGGTGAGGACAGG
FMO1	2326	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	171254528	171254528	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DB-5280-01	TCGA-DB-5280-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69	41			ENST00000354841.4:c.1444G>A	p.Glu482Lys	p.E482K	ENST00000354841	NM_001282692.1	482	Gaa/Aaa	0	0.502	AGGAAAATGGGAAGGAGCCAG
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-DB-5280-01	TCGA-DB-5280-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	66	40			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
IL17RC	84818	hgsc.bcm.edu;broad.mit.edu	GRCh37	3	9959040	9959040	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs112532783	byFrequency	TCGA-DB-5280-01	TCGA-DB-5280-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91	6			ENST00000295981.3:c.41G>A	p.Arg14Gln	p.R14Q	ENST00000295981	NM_153461.3	14	cGa/cAa	0	0.657	GCACTGGGCCGAAGCCCAGTG
HMGN3	9324	hgsc.bcm.edu;ucsc.edu	GRCh37	6	79944270	79944270	+	missense_variant	Missense_Mutation	SNP	T	T	G			TCGA-DB-5280-01	TCGA-DB-5280-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	178	17			ENST00000344726.5:c.8A>C	p.Lys3Thr	p.K3T	ENST00000344726	NM_004242.3	3	aAg/aCg	0	0.502	TACCTTTCTCTTCGGCATAAT
LINGO2	158038	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	27950110	27950110	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DB-5280-01	TCGA-DB-5280-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	65	45			ENST00000379992.2:c.560G>A	p.Cys187Tyr	p.C187Y	ENST00000379992	NM_152570.2	187	tGc/tAc	0	0.483	TGTTAAGTTGCATTTCTCCAG
MYO10	4651	broad.mit.edu;ucsc.edu	GRCh37	5	16694555	16694555	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DB-5280-01	TCGA-DB-5280-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	179	24			ENST00000513610.1:c.3725G>A	p.Arg1242His	p.R1242H	ENST00000513610	NM_012334.2	1242	cGc/cAc	0	0.567	CTTGGACTGGCGGAGGACAAA
LACC1	144811	broad.mit.edu;hgsc.bcm.edu	GRCh37	13	44455647	44455647	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-			TCGA-DB-5280-01	TCGA-DB-5280-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97	51			ENST00000441843.1:c.527delG	p.Gly176GlufsTer3	p.G176Efs*3	ENST00000441843	NM_001128303.1	176	Gga/ga	0	0.328	AGCACTGAGAGGAAAATTAAC
ATRX	546	broad.mit.edu;hgsc.bcm.edu	GRCh37	X	76938749	76938765	+	frameshift_variant	Frame_Shift_Del	DEL	GTCGCCTCAAGGGTGTA	GTCGCCTCAAGGGTGTA	-			TCGA-DB-5280-01	TCGA-DB-5280-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	92	90			ENST00000373344.5:c.1983_1999delTACACCCTTGAGGCGAC	p.Thr662AspfsTer4	p.T662Dfs*4	ENST00000373344	NM_000489.3	661	acTACACCCTTGAGGCGACcg/accg	0	0.373	GTTTCTGTCGGTCGCCTCAAGGGTGTAGTCTTTACAC
ATRX	546	hgsc.bcm.edu	GRCh37	X	76938765	76938765	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-DB-5280-01	TCGA-DB-5280-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	48	6			ENST00000373344.5:c.1983T>C	p.Thr661=	p.T661=	ENST00000373344	NM_000489.3	661	acT/acC	0	0.383	TCAAGGGTGTAGTCTTTACAC
RET	5979	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	43609023	43609023	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-E1-5322-01	TCGA-E1-5322-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21	8			ENST00000355710.3:c.1779A>G	p.Gly593=	p.G593=	ENST00000355710	NM_020975.4	593	ggA/ggG	0	0.642	TTGTTGGGGGACACGAGCCTG
ABTB2	25841	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	34176285	34176285	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-E1-5322-01	TCGA-E1-5322-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	139	108			ENST00000435224.2:c.2729C>T	p.Thr910Ile	p.T910I	ENST00000435224	NM_145804.2	910	aCa/aTa	0	0.592	CATGGATTCTGTTCCTCCGTA
CTTN	2017	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	70261803	70261803	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-E1-5322-01	TCGA-E1-5322-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	362	212			ENST00000376561.3:c.437A>G	p.Glu146Gly	p.E146G	ENST00000376561	NM_001184740.1	146	gAg/gGg	0	0.532	GGGAAGACTGAGAAGCATGCC
CWF19L2	143884	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	107299708	107299708	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-E1-5322-01	TCGA-E1-5322-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	527	42			ENST00000282251.5:c.1250C>A	p.Thr417Lys	p.T417K	ENST00000282251	NM_152434.2	417	aCa/aAa	0	0.418	ACTCCATGATGTTAATCTTTC
LRIG3	121227	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	59271321	59271321	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-E1-5322-01	TCGA-E1-5322-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	81	52			ENST00000320743.3:c.2397G>A	p.Ser799=	p.S799=	ENST00000320743	NM_153377.4	799	tcG/tcA	0	0.562	CATCGTCTAACGATGGGGCTG
TNRC6A	27327	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	24826581	24826581	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-E1-5322-01	TCGA-E1-5322-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	112	71			ENST00000395799.3:c.4786C>T	p.Arg1596Cys	p.R1596C	ENST00000395799	NM_014494.2	1596	Cgt/Tgt	0	0.448	TGGCTGGCCACGTGCCAAATC
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904		TCGA-E1-5322-01	TCGA-E1-5322-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	20	139			ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	0	0.622	TGACTGCTTGTAGATGGCCAT
NEK8	284086	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	27065006	27065006	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-E1-5322-01	TCGA-E1-5322-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57	45			ENST00000268766.6:c.1059C>T	p.Leu353=	p.L353=	ENST00000268766	NM_178170.2	353	ctC/ctT	0	0.701	CTGGGCGTCTCATCCTGTGGG
SESN2	83667	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	28598956	28598956	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-E1-5322-01	TCGA-E1-5322-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	100	63			ENST00000253063.3:c.516C>T	p.Leu172=	p.L172=	ENST00000253063	NM_031459.4	172	ctC/ctT	0	0.652	GGCCATGGCTCATCACCAAGG
HRNR	388697	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	152192510	152192510	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-E1-5322-01	TCGA-E1-5322-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	414	45			ENST00000368801.2:c.1595G>A	p.Arg532Gln	p.R532Q	ENST00000368801	NM_001009931.2	532	cGa/cAa	0	0.567	AGACCCATGTCGGCTGTGTCC
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-E1-5322-01	TCGA-E1-5322-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	118	54			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
DAW1	164781	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	228750104	228750104	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-E1-5322-01	TCGA-E1-5322-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258	19			ENST00000309931.2:c.78G>C	p.Lys26Asn	p.K26N	ENST00000309931	NM_178821.1	26	aaG/aaC	0	0.343	GAGAATTAAAGACTAAGTCCA
OR5H6	79295	hgsc.bcm.edu;broad.mit.edu	GRCh37	3	97983515	97983515	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-E1-5322-01	TCGA-E1-5322-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	290	26			ENST00000383696.2:c.387T>C	p.Phe129=	p.F129=	ENST00000383696	NM_001005479.1	129	ttT/ttC	0	0.368	CAGAATGTTTTCTCTTGGCAA
PDE6B	5158	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	659049	659049	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-E1-5322-01	TCGA-E1-5322-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	56	21			ENST00000496514.1:c.2199A>G	p.Ala733=	p.A733=	ENST00000496514		733	gcA/gcG	0	0.627	TCCAGGTCGCACTTCTCGTGG
FOXP4	116113	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	41554783	41554783	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-E1-5322-01	TCGA-E1-5322-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71	9			ENST00000373060.1:c.547C>T	p.Leu183Phe	p.L183F	ENST00000373060	NM_001012426.1	183	Ctc/Ttc	0	0.662	CCAGCAGCAGCTCCTGCAAAT
LAMA2	3908	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	129475728	129475728	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-E1-5322-01	TCGA-E1-5322-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	111	83			ENST00000421865.2:c.1106G>A	p.Arg369His	p.R369H	ENST00000421865	NM_001079823.1	369	cGt/cAt	0	0.388	TTGAATATACGTGGAAAGTAC
MACC1	346389	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	20198861	20198861	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-E1-5322-01	TCGA-E1-5322-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95	66			ENST00000400331.5:c.1123T>C	p.Tyr375His	p.Y375H	ENST00000400331	NM_182762.3	375	Tat/Cat	0	0.398	TTGGGTCCATAAATTCCAATT
SH2D3C	10044	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	130507277	130507277	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-E1-5322-01	TCGA-E1-5322-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	189	24			ENST00000314830.8:c.1366G>A	p.Ala456Thr	p.A456T	ENST00000314830	NM_170600.2	456	Gcc/Acc	0	0.662	GTCTTTGGGGCACTTCCGGGA
MAP7D3	79649	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	135323365	135323365	+	missense_variant	Missense_Mutation	SNP	T	T	A			TCGA-E1-5322-01	TCGA-E1-5322-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	137	91			ENST00000316077.9:c.489A>T	p.Arg163Ser	p.R163S	ENST00000316077	NM_024597.3	163	agA/agT	0	0.323	CCCATGACCATCTTTTTTGCT
FLOT1	10211	broad.mit.edu;ucsc.edu	GRCh37	6	30708275	30708275	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs139987312	byFrequency	TCGA-E1-5322-01	TCGA-E1-5322-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	143	106			ENST00000376389.3:c.568C>T	p.Arg190Trp	p.R190W	ENST00000376389	NM_005803.2	190	Cgg/Tgg	0	0.532	TCTCTCACCCGGATCCCAGCA
WNT9B	7484	broad.mit.edu;ucsc.edu	GRCh37	17	44953783	44953783	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149931425	by1000genomes	TCGA-E1-5322-01	TCGA-E1-5322-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	89	54			ENST00000290015.2:c.773G>A	p.Arg258His	p.R258H	ENST00000290015	NM_003396.1	258	cGc/cAc	0	0.642	GCCTTGGGCCGCCTAGAGCTG
LIMCH1	22998	broad.mit.edu;ucsc.edu	GRCh37	4	41646515	41646515	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C			TCGA-E1-5322-01	TCGA-E1-5322-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9	10			ENST00000313860.7:c.972-2A>C		p.X324_splice	ENST00000313860	NM_014988.2			0	0.672	CTCCACACTCAGGAGCACCAG
C3P1	388503	broad.mit.edu;ucsc.edu	GRCh37	19	10165979	10165979	+	non_coding_transcript_exon_variant	RNA	SNP	G	G	A			TCGA-E1-5322-01	TCGA-E1-5322-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	116	16			ENST00000497718.1:n.2693G>A		*898*	ENST00000497718				0	0.592	CACCTCCAAGGGGAACCCAGG
OR2T1	26696	broad.mit.edu;hgsc.bcm.edu	GRCh37	1	248570073	248570073	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-			TCGA-E1-5322-01	TCGA-E1-5322-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	164	36			ENST00000366474.1:c.779delC	p.Pro260LeufsTer4	p.P260Lfs*4	ENST00000366474	NM_030904.1	260	Cct/ct	0	0.507	GCTGCTGATTCCTTTCTCTGT
FAM208B	54906	broad.mit.edu;hgsc.bcm.edu	GRCh37	10	5784139	5784140	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-			TCGA-E1-5322-01	TCGA-E1-5322-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	217	70			ENST00000328090.5:c.2407_2408delAA	p.Asn803SerfsTer25	p.N803Sfs*25	ENST00000328090	NM_017782.4	803	AAt/t	0	0.396	GTTTTACAGCAATCAGAACAAA
ATRX	546	broad.mit.edu;hgsc.bcm.edu	GRCh37	X	76944356	76944356	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-			TCGA-E1-5322-01	TCGA-E1-5322-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	231	157			ENST00000373344.5:c.549delA	p.Asp184IlefsTer22	p.D184Ifs*22	ENST00000373344	NM_000489.3	183	aaA/aa	0	0.353	AAATGGAATCTTTTTGAAAAT
ANKK1	255239	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	113267965	113267965	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-7857-01	TCGA-HT-7857-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42	10			ENST00000303941.3:c.858C>T	p.Asp286=	p.D286=	ENST00000303941	NM_178510.1	286	gaC/gaT	0	0.582	TCGAGACAGACATACTGCTGT
FMNL3	91010	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	50043069	50043069	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-HT-7857-01	TCGA-HT-7857-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99	18			ENST00000335154.5:c.2358T>C	p.Tyr786=	p.Y786=	ENST00000335154	NM_175736.4	786	taT/taC	0	0.572	GCTTGAAGCCATACACAGCTC
PTPN11	5781	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	112888197	112888197	+	missense_variant	Missense_Mutation	SNP	T	T	A			TCGA-HT-7857-01	TCGA-HT-7857-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	101	50			ENST00000351677.2:c.213T>A	p.Phe71Leu	p.F71L	ENST00000351677	NM_002834.3	71	ttT/ttA	0	0.418	GGGAGAAATTTGCCACTTTGG
NPAP1	23742	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	24921605	24921605	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-7857-01	TCGA-HT-7857-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47	6			ENST00000329468.2:c.591C>T	p.Asp197=	p.D197=	ENST00000329468	NM_018958.2	197	gaC/gaT	0	0.592	CCCAGGGAGACGTGGCCTCCT
VPS9D1	9605	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	89785502	89785502	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7857-01	TCGA-HT-7857-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	114	19			ENST00000389386.3:c.108C>T	p.Tyr36=	p.Y36=	ENST00000389386	NM_004913.2	36	taC/taT	0	0.552	GGTATTCCGTGTATGCCTCCT
NF1	4763	hgsc.bcm.edu;broad.mit.edu	GRCh37	17	29576001	29576001	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A			TCGA-HT-7857-01	TCGA-HT-7857-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	38	48			ENST00000358273.4:c.3975-1G>A		p.X1325_splice	ENST00000358273	NM_001042492.2			0	0.368	TTTTTTTGTAGGTTAGAACCA
DMRTC2	63946	hgsc.bcm.edu;ucsc.edu	GRCh37	19	42354645	42354645	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-7857-01	TCGA-HT-7857-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	50	28			ENST00000269945.3:c.868C>T	p.Leu290=	p.L290=	ENST00000269945	NM_001040283.1	290	Ctg/Ttg	0	0.637	AGAGTGGCAGCTGCAGCAAGA
ABCA4	24	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	94528252	94528252	+	synonymous_variant	Silent	SNP	G	G	T			TCGA-HT-7857-01	TCGA-HT-7857-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	38	10			ENST00000370225.3:c.1818C>A	p.Gly606=	p.G606=	ENST00000370225	NM_000350.2	606	ggC/ggA	0	0.562	AGGCAAACCCGCCCCAGATGT
TET2	54790	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	106155166	106155166	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7857-01	TCGA-HT-7857-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	43	11			ENST00000380013.4:c.67C>T	p.Pro23Ser	p.P23S	ENST00000380013	NM_001127208.2	23	Ccc/Tcc	0	0.527	ACCATCACCTCCCATTTGCCA
NAA15	80155	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	140262069	140262069	+	stop_gained	Nonsense_Mutation	SNP	G	G	A			TCGA-HT-7857-01	TCGA-HT-7857-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	53	26			ENST00000296543.5:c.248G>A	p.Trp83Ter	p.W83*	ENST00000296543	NM_057175.3	83	tGg/tAg	0	0.363	TCTTTAGGTTGGCACGTTTAT
DUSP22	56940	hgsc.bcm.edu;broad.mit.edu	GRCh37	6	348272	348272	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T			TCGA-HT-7857-01	TCGA-HT-7857-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	140	15			ENST00000344450.5:c.433C>T	p.Gln145Ter	p.Q145*	ENST00000344450	NM_020185.3	145	Cag/Tag	0	0.577	TGAGGTCCATCAGGTAAGCAG
DNAH8	1769	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	38810444	38810444	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7857-01	TCGA-HT-7857-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68	25			ENST00000359357.3:c.3959G>A	p.Arg1320His	p.R1320H	ENST00000359357		1320	cGt/cAt	0	0.323	GAAAGATGTCGTAAACTTCCA
EXOC4	60412	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	133749244	133749244	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7857-01	TCGA-HT-7857-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	80	21			ENST00000253861.4:c.2888A>G	p.Lys963Arg	p.K963R	ENST00000253861	NM_021807.3	963	aAg/aGg	0	0.572	GCTGCCATCAAGCAAGCCACC
UBR5	51366	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	103266680	103266680	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7857-01	TCGA-HT-7857-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	77	11			ENST00000520539.1:c.8250C>T	p.Pro2750=	p.P2750=	ENST00000520539	NM_015902.5	2750	ccC/ccT	0	0.408	TTGTGATTGAGGGCATAGGCT
KLHL25	64410	broad.mit.edu;ucsc.edu	GRCh37	15	86311637	86311637	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7857-01	TCGA-HT-7857-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	140	17			ENST00000337975.5:c.1405G>A	p.Glu469Lys	p.E469K	ENST00000337975	NM_022480.3	469	Gag/Aag	0	0.602	CACCTGTTCTCCGAGGGGTCA
OR10C1	442194	broad.mit.edu;ucsc.edu	GRCh37	6	29407957	29407957	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-HT-7857-01	TCGA-HT-7857-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	164	20			ENST00000444197.2:c.165G>T	p.Gln55His	p.Q55H	ENST00000444197	NM_013941.3	55	caG/caT	0	0.567	CTGCCCTCCAGTCCCCTATGT
EMC10	284361	broad.mit.edu;ucsc.edu	GRCh37	19	50981247	50981247	+	stop_gained	Nonsense_Mutation	SNP	C	C	G			TCGA-HT-7857-01	TCGA-HT-7857-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33	3			ENST00000334976.6:c.176C>G	p.Ser59Ter	p.S59*	ENST00000334976	NM_206538.2	59	tCa/tGa	0	0.607	CTGGAGCACTCATTTGAGATC
PSME4	23198	broad.mit.edu;hgsc.bcm.edu	GRCh37	2	54148047	54148049	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-			TCGA-HT-7857-01	TCGA-HT-7857-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75	22			ENST00000404125.1:c.2239_2241delCCT	p.Pro747del	p.P747del	ENST00000404125	NM_014614.2	747	CCT/-	0	0.374	AGTATTCAGAAGGAGGCTTGTCA
PLA2G15	23659	broad.mit.edu;hgsc.bcm.edu	GRCh37	16	68293167	68293171	+	frameshift_variant	Frame_Shift_Del	DEL	CGTGC	CGTGC	-	rs142263893		TCGA-HT-7857-01	TCGA-HT-7857-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67	16			ENST00000219345.5:c.846_850delCGTGC	p.Phe282LeufsTer22	p.F282Lfs*22	ENST00000219345	NM_012320.3	282	ttCGTGCag/ttag	0	0.58	AGAAGGTGTTCGTGCAGACACCCAC
ATRX	546	broad.mit.edu	GRCh37	X	76814303	76814306	+	frameshift_variant	Frame_Shift_Del	DEL	ATAA	ATAA	-			TCGA-HT-7857-01	TCGA-HT-7857-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68	18			ENST00000373344.5:c.6338_6341delTTAT	p.Phe2113SerfsTer9	p.F2113Sfs*9	ENST00000373344	NM_000489.3	2113	tTTATc/tc	0	0.289	AGTAGAAATGATAAATAATCGTCC
CNNM1	26507	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	101124220	101124220	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-QH-A65Z-01	TCGA-QH-A65Z-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17	9			ENST00000356713.4:c.2075A>G	p.Asn692Ser	p.N692S	ENST00000356713	NM_020348.2	692	aAt/aGt	0	0.423	CGCTTTGAAAATGGAGCCTTT
ACACB	32	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	109616926	109616926	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-QH-A65Z-01	TCGA-QH-A65Z-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	31	17			ENST00000338432.7:c.1471C>G	p.Leu491Val	p.L491V	ENST00000338432		491	Ctc/Gtc	0	0.562	GCCCATCTTTCTCATGAAGCT
ACSF3	197322	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	89180794	89180794	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-QH-A65Z-01	TCGA-QH-A65Z-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	104	33			ENST00000317447.4:c.1025A>G	p.Lys342Arg	p.K342R	ENST00000317447	NM_174917.3	342	aAg/aGg	0	0.647	GTGCTGGAGAAGTGGAAGAAC
MED24	9862	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	38188968	38188968	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-QH-A65Z-01	TCGA-QH-A65Z-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24	23			ENST00000394128.2:c.870C>A	p.Phe290Leu	p.F290L	ENST00000394128	NM_014815.3	290	ttC/ttA	0	0.577	TGAGCCCCACGAAGCAAGCTT
ARRDC5	645432	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	4891396	4891396	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-QH-A65Z-01	TCGA-QH-A65Z-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39	13			ENST00000381781.2:c.691C>G	p.Gln231Glu	p.Q231E	ENST00000381781	NM_001080523.1	231	Cag/Gag	0	0.587	CCCTCGTACTGTATGTGGGCA
PPP1R13L	10848	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	45895364	45895364	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-QH-A65Z-01	TCGA-QH-A65Z-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	59	12			ENST00000418234.2:c.1589C>T	p.Ala530Val	p.A530V	ENST00000418234	NM_001142502.1	530	gCc/gTc	0	0.687	CACAGCAGGGGCCTGCTCCAT
EXTL1	2134	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	26349229	26349229	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-QH-A65Z-01	TCGA-QH-A65Z-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11	31			ENST00000374280.3:c.92G>A	p.Arg31His	p.R31H	ENST00000374280	NM_004455.2	31	cGc/cAc	0	0.657	TCCCTTCTCCGCCTGGCATTG
G0S2	50486	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	209849305	209849305	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-QH-A65Z-01	TCGA-QH-A65Z-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28	13			ENST00000367029.4:c.276C>T	p.Gly92=	p.G92=	ENST00000367029	NM_015714.3	92	ggC/ggT	0	0.667	CGGTCCTCGGCGGCCGGGCCC
RYR2	6262	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	237957283	237957283	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-QH-A65Z-01	TCGA-QH-A65Z-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21	16			ENST00000366574.2:c.13899C>T	p.Leu4633=	p.L4633=	ENST00000366574	NM_001035.2	4633	ctC/ctT	0	0.363	GGGATAGACTCGTAATCAACA
LAMA5	3911	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	20	60888747	60888747	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-QH-A65Z-01	TCGA-QH-A65Z-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96	76			ENST00000252999.3:c.8616C>T	p.Asp2872=	p.D2872=	ENST00000252999	NM_005560.4	2872	gaC/gaT	0	0.662	AGACGAAGTCGTCTGGCCGCA
FZD7	8324	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	202900715	202900715	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-QH-A65Z-01	TCGA-QH-A65Z-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	103	41			ENST00000286201.1:c.1345C>T	p.Arg449Cys	p.R449C	ENST00000286201	NM_003507.1	449	Cgt/Tgt	0	0.612	GTCCCTCTTCCGTATCCGCAC
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-QH-A65Z-01	TCGA-QH-A65Z-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39	25			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
ECT2	1894	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	172501694	172501694	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-QH-A65Z-01	TCGA-QH-A65Z-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23	18			ENST00000392692.3:c.1723C>T	p.Leu575Phe	p.L575F	ENST00000392692	NM_001258315.1	575	Ctc/Ttc	0	0.274	TCATGCTTTTCTCAAGGTAAT
ABCE1	6059	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	146044497	146044497	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-QH-A65Z-01	TCGA-QH-A65Z-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33	41			ENST00000296577.4:c.1505G>A	p.Arg502Gln	p.R502Q	ENST00000296577	NM_002940.2	502	cGa/cAa	0	0.383	ATGGCAGCTCGAGTTGTCAAA
PHF3	23469	hgsc.bcm.edu;broad.mit.edu	GRCh37	6	64423124	64423124	+	synonymous_variant	Silent	SNP	C	C	G			TCGA-QH-A65Z-01	TCGA-QH-A65Z-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	155	12			ENST00000262043.3:c.5640C>G	p.Gly1880=	p.G1880=	ENST00000262043		1880	ggC/ggG	0	0.507	GGTATATAGGCCCGCAGAATT
SLC26A4	5172	hgsc.bcm.edu;broad.mit.edu	GRCh37	7	107314667	107314667	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-QH-A65Z-01	TCGA-QH-A65Z-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	85	5			ENST00000265715.3:c.474C>T	p.Asp158=	p.D158=	ENST00000265715	NM_000441.1	158	gaC/gaT	0	0.433	TGGCCCCCGACGAACACTTTC
SVEP1	79987	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	113194246	113194246	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-QH-A65Z-01	TCGA-QH-A65Z-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75	29			ENST00000401783.2:c.5302T>C	p.Tyr1768His	p.Y1768H	ENST00000401783	NM_153366.3	1768	Tac/Cac	0	0.378	GAACATATGTAGGATCCATCT
XPNPEP2	7512	broad.mit.edu;ucsc.edu	GRCh37	X	128879232	128879232	+	synonymous_variant	Silent	SNP	A	A	T			TCGA-QH-A65Z-01	TCGA-QH-A65Z-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	31	3			ENST00000371106.3:c.288A>T	p.Thr96=	p.T96=	ENST00000371106	NM_003399.5	96	acA/acT	0	0.488	CAGGCTTTACAGGGTCTGCAG
TACR3	6870	broad.mit.edu;ucsc.edu	GRCh37	4	104510918	104510918	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-QH-A65Z-01	TCGA-QH-A65Z-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	107	70			ENST00000304883.2:c.1319C>T	p.Ser440Phe	p.S440F	ENST00000304883	NM_001059.2	440	tCt/tTt	0	0.478	ATTCCTGCGAGAGCAGCCATT
CREB3	10488	broad.mit.edu;ucsc.edu	GRCh37	9	35736644	35736644	+	missense_variant	Missense_Mutation	SNP	A	A	C			TCGA-QH-A65Z-01	TCGA-QH-A65Z-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	199	75			ENST00000353704.2:c.1037A>C	p.Gln346Pro	p.Q346P	ENST00000353704	NM_006368.4	346	cAg/cCg	0	0.567	CTCCCCCTGCAGGCAAATCTC
ITSN1	6453	broad.mit.edu;ucsc.edu	GRCh37	21	35183494	35183494	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-QH-A65Z-01	TCGA-QH-A65Z-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	105	40			ENST00000381318.3:c.2535G>A	p.Thr845=	p.T845=	ENST00000381318	NM_003024.2	845	acG/acA	0	0.547	AGCCCTCCACGACCCCTAATA
SLC1A7	6512	broad.mit.edu;hgsc.bcm.edu	GRCh37	1	53553683	53553684	+	frameshift_variant,stop_lost	Frame_Shift_Del	DEL	AG	AG	-			TCGA-QH-A65Z-01	TCGA-QH-A65Z-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	20	18			ENST00000371494.4:c.1680_1681delCT	p.Ter561SerfsTer41	p.*561Sfs*41	ENST00000371494	NM_006671.4	560	gtCTga/gtga	0	0.663	CCGCAGGCTCAGACATTGGTCT
CTNNB1	1499	broad.mit.edu;hgsc.bcm.edu	GRCh37	3	41275294	41275294	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-			TCGA-QH-A65Z-01	TCGA-QH-A65Z-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	164	105			ENST00000349496.5:c.1461delT	p.His488ThrfsTer19	p.H488Tfs*19	ENST00000349496	NM_001904.3	487	cTt/ct	0	0.493	GCAGTTCGCCTTCACTATGGA
PRAG1	157285	broad.mit.edu;hgsc.bcm.edu	GRCh37	8	8234817	8234819	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-			TCGA-QH-A65Z-01	TCGA-QH-A65Z-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26	15			ENST00000520004.1:c.1100_1102delTGA	p.Met367del	p.M367del	ENST00000520004		367	aTGAag/aag	0	0.68	GCAGGTTCCTTCATGAGGGAGCA
KAT6B	23522	broad.mit.edu;hgsc.bcm.edu	GRCh37	10	76784946	76784949	+	frameshift_variant	Frame_Shift_Del	DEL	ACAA	ACAA	-			TCGA-QH-A65Z-01	TCGA-QH-A65Z-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37	14			ENST00000287239.4:c.3606_3609delAACA	p.Thr1203ArgfsTer21	p.T1203Rfs*21	ENST00000287239	NM_001256468.1	1201	agACAA/ag	0	0.451	GGAAGAAAAGACAAACAGAGGAAG
RBBP6	5930	broad.mit.edu;hgsc.bcm.edu	GRCh37	16	24567746	24567747	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A			TCGA-QH-A65Z-01	TCGA-QH-A65Z-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	50	14			ENST00000319715.4:c.653dupA	p.Tyr218Ter	p.Y218*	ENST00000319715	NM_006910.4	218	tat/tAat	0	0.401	CACTGGAAAATATGCAATACCA
ZACN	353174	broad.mit.edu;hgsc.bcm.edu	GRCh37	17	74075804	74075805	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC			TCGA-QH-A65Z-01	TCGA-QH-A65Z-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	55	21			ENST00000334586.5:c.245_246dupCC	p.Ser83ProfsTer58	p.S83Pfs*58	ENST00000334586	NM_180990.3	82	tcc/tCCcc	0	0.569	ATACACAATGTCCTCCATGCTG
CIC	23152	broad.mit.edu;hgsc.bcm.edu	GRCh37	19	42797776	42797777	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-			TCGA-QH-A65Z-01	TCGA-QH-A65Z-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7	10			ENST00000575354.2:c.3831_3832delCG	p.Val1278ProfsTer65	p.V1278Pfs*65	ENST00000575354	NM_015125.3	1276	tgGCgc/tggc	0	0.649	CTTCAGACTGGCGCGTCCCTGG
CIC	23152	broad.mit.edu	GRCh37	19	42798989	42798990	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs148444899		TCGA-QH-A65Z-01	TCGA-QH-A65Z-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71	8			ENST00000575354.2:c.4473_4474insA	p.Ala1492SerfsTer22	p.A1492Sfs*22	ENST00000575354	NM_015125.3	1491	-/A	0	0.574	AGGCCACAGCCGCCTTCCAGGC
CAMK1D	57118	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	12803041	12803041	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-6407-01	TCGA-DU-6407-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23	13			ENST00000378847.3:c.394G>A	p.Val132Met	p.V132M	ENST00000378847	NM_153498.2	132	Gtg/Atg	0	0.577	CTTGGACGCCGTGTACTATCT
MYO3A	53904	hgsc.bcm.edu;broad.mit.edu	GRCh37	10	26359114	26359114	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-DU-6407-01	TCGA-DU-6407-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75	4			ENST00000265944.5:c.1245T>C	p.Tyr415=	p.Y415=	ENST00000265944	NM_017433.4	415	taT/taC	0	0.318	ACTTAGGATATCAATCTATGA
HPS1	3257	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	100185433	100185433	+	missense_variant	Missense_Mutation	SNP	A	A	C			TCGA-DU-6407-01	TCGA-DU-6407-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	25	15			ENST00000325103.6:c.1200T>G	p.Asp400Glu	p.D400E	ENST00000325103	NM_000195.3	400	gaT/gaG	0	0.692	TGGAGAAGCCATCCATCAGCT
CBX5	23468	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	54635636	54635636	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-6407-01	TCGA-DU-6407-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	72	45			ENST00000209875.4:c.479G>A	p.Cys160Tyr	p.C160Y	ENST00000209875	NM_012117.2	160	tGt/tAt	0	0.398	AATTTGTGGACATTTCACATT
MIPEP	4285	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	13	24444199	24444199	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-6407-01	TCGA-DU-6407-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62	54			ENST00000382172.3:c.739G>A	p.Asp247Asn	p.D247N	ENST00000382172	NM_005932.3	247	Gat/Aat	0	0.393	ATGATATGATCCCCAGCAGAT
ZDHHC7	55625	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	85010046	85010046	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-6407-01	TCGA-DU-6407-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24	17			ENST00000564466.1:c.941G>A	p.Gly314Glu	p.G314E	ENST00000564466	NM_001145548.1	314	gGg/gAg	0	0.572	TGAGGGGGGCCCCCCAAAGAC
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7579362	7579362	+	missense_variant	Missense_Mutation	SNP	A	A	C			TCGA-DU-6407-01	TCGA-DU-6407-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7	54			ENST00000269305.4:c.325T>G	p.Phe109Val	p.F109V	ENST00000269305	NM_001126112.2	109	Ttc/Gtc	0	0.612	CCCAGACGGAAACCGTAGCTG
ACACA	31	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	35640173	35640173	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-DU-6407-01	TCGA-DU-6407-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45	15			ENST00000353139.5:c.605A>G	p.Asn202Ser	p.N202S	ENST00000353139	NM_198834.1	202	aAt/aGt	0	0.408	CTCACCTGCATTGGCTTTAAG
HNF1B	6928	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	36059196	36059196	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DU-6407-01	TCGA-DU-6407-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	43	7			ENST00000225893.4:c.1539C>T	p.Tyr513=	p.Y513=	ENST00000225893	NM_001165923.1	513	taC/taT	0	0.532	GCTTGTGTGCGTACACTGGAG
FPGT	8790	hgsc.bcm.edu;ucsc.edu	GRCh37	1	74670899	74670899	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-DU-6407-01	TCGA-DU-6407-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68	11			ENST00000609362.1:c.1168C>A	p.Pro390Thr	p.P390T	ENST00000609362		390	Cca/Aca	0	0.388	TAGTATCTTTCCAGATATACC
USP25	29761	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	21	17246819	17246819	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-DU-6407-01	TCGA-DU-6407-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	182	34			ENST00000285679.6:c.2773T>C	p.Ser925Pro	p.S925P	ENST00000285679	NM_013396.3	925	Tca/Cca	0	0.328	AGAATTGATATCACATTATAG
CYP26B1	56603	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	72359586	72359586	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-6407-01	TCGA-DU-6407-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17	20			ENST00000001146.2:c.1309G>A	p.Gly437Ser	p.G437S	ENST00000001146	NM_019885.3	437	Ggt/Agt	0	0.647	GTCCGGACACCGCCACCGAAC
SCN1A	6323	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	166872165	166872165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146374754		TCGA-DU-6407-01	TCGA-DU-6407-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	87	54			ENST00000303395.4:c.3502G>A	p.Val1168Ile	p.V1168I	ENST00000303395		1168	Gta/Ata	0	0.413	GGTTCCACTACGGGCTGTTCT
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-DU-6407-01	TCGA-DU-6407-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	38	24			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
LMCD1	29995	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	8590439	8590439	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-DU-6407-01	TCGA-DU-6407-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	70	34			ENST00000157600.3:c.573C>T	p.Ser191=	p.S191=	ENST00000157600	NM_014583.3	191	agC/agT	0	0.587	AATATAAGAGCGAGGCCCTCG
FAM134B	54463	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	16475174	16475174	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-DU-6407-01	TCGA-DU-6407-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52	38			ENST00000306320.9:c.1170G>A	p.Thr390=	p.T390=	ENST00000306320	NM_001034850.2	390	acG/acA	0	0.493	CTGCTGATTGCGTCTCTTTGC
CHDC2	286464	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	36091355	36091355	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-DU-6407-01	TCGA-DU-6407-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64	30			ENST00000313548.4:c.290C>A	p.Ser97Tyr	p.S97Y	ENST00000313548	NM_173695.2	97	tCt/tAt	0	0.433	CAATTCCTTTCTCTTGAGGAA
HNRNPH2	3188	hgsc.bcm.edu;broad.mit.edu	GRCh37	X	100667035	100667035	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-DU-6407-01	TCGA-DU-6407-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99	5			ENST00000316594.5:c.59G>T	p.Trp20Leu	p.W20L	ENST00000316594	NM_001199974.1	20	tGg/tTg	0	0.527	GGCCTACCCTGGTCCTGCTCA
IGF2R	3482	broad.mit.edu;ucsc.edu	GRCh37	6	160501242	160501242	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-6407-01	TCGA-DU-6407-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	50	44			ENST00000356956.1:c.5768C>T	p.Ala1923Val	p.A1923V	ENST00000356956	NM_000876.2	1923	gCg/gTg	0	0.557	GAGAGCAGGGCGAAGCTGTGG
GATA3	2625	broad.mit.edu;ucsc.edu	GRCh37	10	8100437	8100437	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DU-6407-01	TCGA-DU-6407-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39	33			ENST00000346208.3:c.411G>A	p.Ser137=	p.S137=	ENST00000346208		137	tcG/tcA	0	0.716	CCCCGGCCTCGTCCTCCTCCT
HELZ	9931	broad.mit.edu;ucsc.edu	GRCh37	17	65105677	65105677	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-DU-6407-01	TCGA-DU-6407-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42	43			ENST00000358691.5:c.4044T>C	p.Ala1348=	p.A1348=	ENST00000358691	NM_014877.3	1348	gcT/gcC	0	0.473	GTGCGTGGGGAGCAGGAAGGG
PDK1	5163	broad.mit.edu;ucsc.edu	GRCh37	2	173423525	173423525	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-DU-6407-01	TCGA-DU-6407-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42	30			ENST00000282077.3:c.286C>G	p.Leu96Val	p.L96V	ENST00000282077		96	Ctc/Gtc	0	0.393	AGAAATAAGTCTCCTTCCAGA
ATRX	546	broad.mit.edu;hgsc.bcm.edu	GRCh37	X	76939340	76939343	+	frameshift_variant	Frame_Shift_Del	DEL	CTAC	CTAC	-			TCGA-DU-6407-01	TCGA-DU-6407-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	277	132			ENST00000373344.5:c.1405_1408delGTAG	p.Val469IlefsTer44	p.V469Ifs*44	ENST00000373344	NM_000489.3	469	GTAGat/at	0	0.358	TGCTCACTATCTACCTGTTTTCTT
PLAC9	219348	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	81901857	81901857	+	synonymous_variant	Silent	SNP	T	T	A			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57	10			ENST00000372263.3:c.84T>A	p.Pro28=	p.P28=	ENST00000372263	NM_001012973.1	28	ccT/ccA	0	0.532	CCTTCAGCCCTCCGCGAGGAG
OR4S2	219431	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	55419308	55419308	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90	62			ENST00000312422.2:c.929G>T	p.Gly310Val	p.G310V	ENST00000312422	NM_001004059.2	310	gGg/gTg	0	0.363	GAGGCTAAAGGGAAATAGTTG
FAT3	120114	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	92624025	92624025	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40	23			ENST00000298047.6:c.13516G>T	p.Val4506Leu	p.V4506L	ENST00000298047		4506	Gtg/Ttg	0	0.582	AACGGATTTGGTGGGCCCGCC
TUBGCP3	10426	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	13	113181323	113181323	+	synonymous_variant	Silent	SNP	A	A	C			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42	9			ENST00000261965.3:c.1488T>G	p.Val496=	p.V496=	ENST00000261965	NM_006322.4	496	gtT/gtG	0	0.398	GATCATGACAAACTTGGTGCA
DLGAP5	9787	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	14	55643912	55643912	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	13	19			ENST00000247191.2:c.917C>T	p.Ser306Phe	p.S306F	ENST00000247191	NM_014750.4	306	tCc/tTc	0	0.383	AGGTGCAAAGGAATTCTTCCC
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9	74			ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	0	0.642	GCAGCGCTCATGGTGGGGGCA
MYO15A	51168	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	18022907	18022907	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68	41			ENST00000205890.5:c.793G>A	p.Gly265Ser	p.G265S	ENST00000205890	NM_016239.3	265	Ggc/Agc	0	0.652	GGCGGGCCTCGGCCCCTACAG
VEZF1	7716	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	56060673	56060673	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	94	77			ENST00000581208.1:c.115G>C	p.Asp39His	p.D39H	ENST00000581208	NM_007146.2	39	Gat/Cat	0	0.473	GGTTTCTGATCAGGGGGCTCC
DNAI2	64446	hgsc.bcm.edu;broad.mit.edu	GRCh37	17	72301394	72301394	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	111	11			ENST00000446837.2:c.1024G>A	p.Val342Ile	p.V342I	ENST00000446837		342	Gtc/Atc	0	0.577	GCAGGGCATCGTCATCTCCTG
NUDT19	390916	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	33183087	33183087	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36	9			ENST00000397061.3:c.221C>T	p.Ala74Val	p.A74V	ENST00000397061	NM_001105570.1	74	gCg/gTg	0	0.751	GACCGCTCGGCGGACTGGCTG
CROCC	9696	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	17264170	17264170	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs141704732		TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	34	6			ENST00000375541.5:c.1228G>C	p.Glu410Gln	p.E410Q	ENST00000375541	NM_014675.3	410	Gag/Cag	0	0.572	GAAGCGTCTTGAGAAGCAGAA
FCRL5	83416	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	157514077	157514077	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	155	134			ENST00000361835.3:c.819C>A	p.Ser273Arg	p.S273R	ENST00000361835	NM_001195388.1	273	agC/agA	0	0.512	AGGATCTCGGGCTGTCAGATA
PTGS2	5743	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	186643728	186643728	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	111	21			ENST00000367468.5:c.1572T>C	p.Val524=	p.V524=	ENST00000367468	NM_000963.2	524	gtT/gtC	0	0.458	GAGAACATATAACATTACCCA
LAD1	3898	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	201352455	201352455	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	201	70			ENST00000391967.2:c.1238C>T	p.Thr413Met	p.T413M	ENST00000391967	NM_005558.3	413	aCg/aTg	0	0.597	CCGTATGGCCGTGTGGTATCT
RYR2	6262	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	237804274	237804274	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14	19			ENST00000366574.2:c.7193T>C	p.Leu2398Pro	p.L2398P	ENST00000366574	NM_001035.2	2398	cTc/cCc	0	0.453	TTGATTGACCTCTTGGGACGC
SPATA2	9825	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	20	48523042	48523042	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	51	18			ENST00000422556.1:c.677C>T	p.Ser226Leu	p.S226L	ENST00000422556	NM_001135773.1	226	tCa/tTa	0	0.672	TGCCACTCGTGACATGGAGGC
SCUBE1	80274	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	22	43606074	43606074	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	16	47			ENST00000360835.4:c.2556C>T	p.Gly852=	p.G852=	ENST00000360835	NM_173050.3	852	ggC/ggT	0	0.632	CCAGAACATCGCCGCACTCAT
GPR45	11250	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	105858985	105858985	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67	23			ENST00000258456.1:c.670A>G	p.Lys224Glu	p.K224E	ENST00000258456	NM_007227.3	224	Aag/Gag	0	0.672	CACGGTCCGCAAGAACGCCGT
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	179588855	179588855	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8	13			ENST00000589042.1:c.21131C>T	p.Pro7044Leu	p.P7044L	ENST00000589042	NM_001267550.1	7044	cCc/cTc	0	0.423	TGTGAAAGAGGGAGGAACTGC
DNAH7	56171	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	196749379	196749379	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45	16			ENST00000312428.6:c.5693C>T	p.Thr1898Ile	p.T1898I	ENST00000312428	NM_018897.2	1898	aCa/aTa	0	0.358	CTTTGAGGATGTTTGCTCAGT
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26	28			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
ANKMY1	51281	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	241468460	241468460	+	missense_variant	Missense_Mutation	SNP	T	T	G			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	124	26			ENST00000391987.1:c.680A>C	p.Lys227Thr	p.K227T	ENST00000391987		227	aAg/aCg	0	0.522	TCACCTGAACTTGTAAGTTTG
NBEAL2	23218	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	47038035	47038035	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	16	7			ENST00000450053.3:c.2426T>C	p.Phe809Ser	p.F809S	ENST00000450053	NM_015175.2	809	tTt/tCt	0	0.657	GTGGCCATCTTTCACGAAGCC
P2RY12	64805	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	151056104	151056104	+	missense_variant	Missense_Mutation	SNP	A	A	T			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	54	22			ENST00000302632.3:c.530T>A	p.Phe177Tyr	p.F177Y	ENST00000302632	NM_022788.4	177	tTc/tAc	0	0.368	TGATTTAAGGAAAGAGCATTT
RGS12	6002	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	3318009	3318009	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184	19			ENST00000344733.5:c.112G>A	p.Gly38Arg	p.G38R	ENST00000344733	NM_198229.2	38	Gga/Aga	0	0.637	CACGCTTTCGGGACAGGCACC
FRYL	285527	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	48536663	48536663	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	16	37			ENST00000358350.4:c.6604C>T	p.Leu2202=	p.L2202=	ENST00000358350	NM_015030.1	2202	Cta/Tta	0	0.313	ATAATCTGTAGTAATGATTGC
C4orf21	55345	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	113475127	113475127	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	133	16			ENST00000505019.1:c.5210G>T	p.Gly1737Val	p.G1737V	ENST00000505019	NM_018392.4	1737	gGc/gTc	0	0.313	ATTTTCTGAGCCAGCATGCAA
BBS12	166379	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	123664898	123664898	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45	16			ENST00000542236.1:c.1851A>G	p.Thr617=	p.T617=	ENST00000542236	NM_001178007.1	617	acA/acG	0	0.363	AAGCCAGCACATACATTCAAC
TRIML2	205860	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	189018488	189018488	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64	44			ENST00000512729.1:c.484T>C	p.Ser162Pro	p.S162P	ENST00000512729	NM_173553.1	162	Tct/Cct	0	0.383	CTTTCTAAAGAGTATTTTGCA
CDH9	1007	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	26881636	26881636	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	131	40			ENST00000231021.4:c.1979A>G	p.Asn660Ser	p.N660S	ENST00000231021	NM_016279.3	660	aAc/aGc	0	0.428	GCCTTCATCGTTGTAGGTCAC
EGFLAM	133584	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	38338820	38338820	+	synonymous_variant	Silent	SNP	C	C	T	rs142461042		TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29	27			ENST00000354891.3:c.228C>T	p.Gly76=	p.G76=	ENST00000354891	NM_001205301.1	76	ggC/ggT	0	0.532	CTGAGGTTGGCGCAGATAAAT
SLC26A2	1836	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	149357883	149357883	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39	49			ENST00000286298.4:c.668G>A	p.Ser223Asn	p.S223N	ENST00000286298	NM_000112.3	223	aGc/aAc	0	0.353	ATGGTTGGCAGCACTGTAACC
PGK2	5232	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	49754106	49754106	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	143	26			ENST00000304801.3:c.795C>T	p.Ile265=	p.I265=	ENST00000304801	NM_138733.4	265	atC/atT	0	0.418	TATCTTTAACGATCTTGGCTC
RIMS1	22999	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	72967911	72967911	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	20	12			ENST00000521978.1:c.2854C>T	p.Arg952Cys	p.R952C	ENST00000521978	NM_014989.5	952	Cgt/Tgt	0	0.463	TCACCGCTCACGTTCAGTATC
TTK	7272	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	80720598	80720598	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	44	22			ENST00000369798.2:c.537G>A	p.Met179Ile	p.M179I	ENST00000369798	NM_003318.4	179	atG/atA	0	0.348	CACTAGAAATGCTGGAAATTG
CARD11	84433	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	2963945	2963945	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71	32			ENST00000396946.4:c.1862C>T	p.Ser621Phe	p.S621F	ENST00000396946	NM_032415.4	621	tCc/tTc	0	0.607	TTGGTGGGAGGAGGAGGAGGA
DBNL	28988	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	44097451	44097451	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	46	27			ENST00000468694.1:c.545A>G	p.Lys182Arg	p.K182R	ENST00000468694	NM_001122956.1	182	aAa/aGa	0	0.547	TTCTGGGCCAAAGCAGAGGTG
TRIP6	7205	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	100465834	100465834	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	44	23			ENST00000200457.4:c.342G>A	p.Ala114=	p.A114=	ENST00000200457	NM_003302.2	114	gcG/gcA	0	0.662	GGGGTCATGCGTCACGGCGAC
LRRC4	64101	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	127668930	127668930	+	synonymous_variant	Silent	SNP	G	G	C	rs139849197		TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23	20			ENST00000249363.3:c.1764C>G	p.Ser588=	p.S588=	ENST00000249363	NM_022143.4	588	tcC/tcG	0	0.547	CTGATACACCGGACGGAgctg
PSD3	23362	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	18729531	18729531	+	synonymous_variant	Silent	SNP	T	T	A			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	119	24			ENST00000327040.8:c.843A>T	p.Pro281=	p.P281=	ENST00000327040	NM_015310.3	281	ccA/ccT	0	0.567	CACATCCCCCTGGGTGCTCTC
FUT10	84750	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	33246920	33246920	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88	66			ENST00000327671.5:c.773A>G	p.Asn258Ser	p.N258S	ENST00000327671	NM_032664.3	258	aAt/aGt	0	0.438	AGAGGCTGGATTTTTCAGCTG
ADAM2	2515	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	39624672	39624672	+	splice_region_variant,synonymous_variant	Splice_Region	SNP	T	T	C			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88	80			ENST00000265708.4:c.1311A>G	p.Leu437=	p.L437=	ENST00000265708	NM_001464.4	437	ctA/ctG	0	0.343	AAGCTCTTACTAGACAGTTTT
FPGS	2356	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	130569293	130569293	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	151	40			ENST00000373247.2:c.428A>G	p.Asn143Ser	p.N143S	ENST00000373247	NM_004957.4	143	aAt/aGt	0	0.657	ATCCGCATCAATGGGCAGCCC
ZER1	10444	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	131503855	131503855	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	187	39			ENST00000291900.2:c.1696C>T	p.Leu566Phe	p.L566F	ENST00000291900	NM_006336.3	566	Ctc/Ttc	0	0.567	TTGAAATTGAGGAACATCTCG
ATRX	546	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	76940500	76940500	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5	47			ENST00000373344.5:c.595-2A>C		p.X199_splice	ENST00000373344	NM_000489.3			0	0.294	AAAGCAATTCTATTAAAAGAA
ACTRT1	139741	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	127185376	127185376	+	synonymous_variant	Silent	SNP	G	G	T			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30	49			ENST00000371124.3:c.810C>A	p.Ile270=	p.I270=	ENST00000371124	NM_138289.3	270	atC/atA	0	0.512	CTGGGCTGTGGATGCCCAGCT
OR51D1	390038	broad.mit.edu;ucsc.edu	GRCh37	11	4661741	4661741	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-HT-7477-01	TCGA-HT-7477-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	38	17			ENST00000357605.2:c.721C>A	p.Leu241Met	p.L241M	ENST00000357605	NM_001004751.2	241	Ctg/Atg	0	0.512	TGTTTTGGAGCTGTCCTCTCG
KCNK18	338567	hgsc.bcm.edu;broad.mit.edu	GRCh37	10	118957048	118957048	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-7608-01	TCGA-HT-7608-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76	5			ENST00000334549.1:c.49C>T	p.Leu17=	p.L17=	ENST00000334549	NM_181840.1	17	Ctg/Ttg	0	0.632	CCCAGAGGCCCTGGGAAAGCT
PRPF40B	25766	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	50036431	50036431	+	synonymous_variant	Silent	SNP	C	C	G			TCGA-HT-7608-01	TCGA-HT-7608-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	32	29			ENST00000548825.2:c.2091C>G	p.Leu697=	p.L697=	ENST00000548825	NM_001031698.2	697	ctC/ctG	0	0.557	GGATCCGGCTCTTCCGGGAGT
EIF2B1	1967	hgsc.bcm.edu;broad.mit.edu	GRCh37	12	124111689	124111689	+	synonymous_variant	Silent	SNP	G	G	A	rs146748240	byFrequency	TCGA-HT-7608-01	TCGA-HT-7608-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	138	9			ENST00000424014.2:c.384C>T	p.His128=	p.H128=	ENST00000424014	NM_001414.3	128	caC/caT	0	0.562	TGGAGTAGGCGTGAGTCAATA
TSHR	7253	hgsc.bcm.edu;broad.mit.edu	GRCh37	14	81609744	81609744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146403935	by1000genomes	TCGA-HT-7608-01	TCGA-HT-7608-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	202	14			ENST00000298171.2:c.1342G>A	p.Val448Ile	p.V448I	ENST00000298171	NM_000369.2	448	Gtc/Atc	0	0.517	CAAACTGAACGTCCCCCGCTT
KLHL25	64410	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	86312652	86312652	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7608-01	TCGA-HT-7608-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	60	10			ENST00000337975.5:c.390C>T	p.His130=	p.H130=	ENST00000337975	NM_022480.3	130	caC/caT	0	0.622	CCCGCACATCGTGGAACTGCA
MYH8	4626	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	10299697	10299697	+	stop_gained	Nonsense_Mutation	SNP	G	G	A			TCGA-HT-7608-01	TCGA-HT-7608-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28	6			ENST00000403437.2:c.4603C>T	p.Gln1535Ter	p.Q1535*	ENST00000403437	NM_002472.2	1535	Caa/Taa	0	0.383	TGTTCTACTTGCTTCTTTATT
KRT15	3866	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	39673185	39673185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138271368		TCGA-HT-7608-01	TCGA-HT-7608-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	89	14			ENST00000254043.3:c.613G>A	p.Val205Ile	p.V205I	ENST00000254043	NM_002275.3	205	Gtt/Att	0	0.612	TCAGCCTCAACGCCCTGGCGC
DNM2	1785	hgsc.bcm.edu;ucsc.edu	GRCh37	19	10908139	10908139	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-HT-7608-01	TCGA-HT-7608-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78	24			ENST00000389253.4:c.1280G>T	p.Cys427Phe	p.C427F	ENST00000389253	NM_001005361.2	427	tGt/tTt	0	0.517	AGTTTGAAGTGTGTTGATCTC
AXL	558	hgsc.bcm.edu;broad.mit.edu	GRCh37	19	41763470	41763470	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7608-01	TCGA-HT-7608-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	116	6			ENST00000301178.4:c.2269G>A	p.Glu757Lys	p.E757K	ENST00000301178	NM_021913.4	757	Gag/Aag	0	0.557	GGAGAACAGCGAGATTTATGA
C1orf65	164127	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	223567391	223567391	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7608-01	TCGA-HT-7608-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82	64			ENST00000366875.3:c.574C>T	p.Arg192Trp	p.R192W	ENST00000366875	NM_152610.2	192	Cgg/Tgg	0	0.597	TCCCTCGGAGCGGTCTTCTGT
RIPK4	54101	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	21	43161859	43161859	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7608-01	TCGA-HT-7608-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	136	12			ENST00000332512.3:c.1494C>T	p.Asn498=	p.N498=	ENST00000332512	NM_020639.2	498	aaC/aaT	0	0.632	CATCCTTGGCGTTGACACTGA
TOP3B	8940	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	22	22322990	22322990	+	splice_donor_variant	Splice_Site	SNP	C	C	A			TCGA-HT-7608-01	TCGA-HT-7608-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76	22			ENST00000398793.2:c.738+1G>T		p.X246_splice	ENST00000398793	NM_003935.3			0	0.552	AGGCAAGGAACCTTGGCCTGC
RASD2	23551	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	22	35947956	35947956	+	synonymous_variant	Silent	SNP	C	C	T	rs144245051		TCGA-HT-7608-01	TCGA-HT-7608-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52	24			ENST00000216127.4:c.678C>T	p.Asp226=	p.D226=	ENST00000216127	NM_014310.3	226	gaC/gaT	0	0.642	AGGAGATGGACGCCTATGGCA
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HT-7608-01	TCGA-HT-7608-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79	43			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
OTOP1	133060	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	4199681	4199681	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7608-01	TCGA-HT-7608-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91	38			ENST00000296358.4:c.880C>T	p.Arg294Cys	p.R294C	ENST00000296358	NM_177998.1	294	Cgc/Tgc	0	0.567	TCAACTTTGCGCCCGATGTTC
IL17F	112744	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	52103580	52103580	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7608-01	TCGA-HT-7608-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52	35			ENST00000336123.4:c.202G>A	p.Val68Ile	p.V68I	ENST00000336123	NM_052872.3	68	Gtt/Att	0	0.448	GACATGGAAACGCGCTGGTTT
AP1S1	1174	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	100799992	100799992	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-HT-7608-01	TCGA-HT-7608-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	19	5			ENST00000337619.5:c.121G>C	p.Ala41Pro	p.A41P	ENST00000337619	NM_001283.3	41	Gct/Cct	0	0.537	GGTTGTCCTGGCTCGAAAGCC
TIGIT	201633	broad.mit.edu;ucsc.edu	GRCh37	3	114026861	114026861	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-HT-7608-01	TCGA-HT-7608-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91	45			ENST00000486257.1:c.618A>G	p.Ala206=	p.A206=	ENST00000486257		206	gcA/gcG	0	0.572	CAGAAGCTGCACCTGCTGGGC
LMNA	4000	broad.mit.edu;ucsc.edu	GRCh37	1	156104684	156104684	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7608-01	TCGA-HT-7608-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	85	20			ENST00000368300.4:c.728A>G	p.Asp243Gly	p.D243G	ENST00000368300	NM_170707.3	243	gAt/gGt	0	0.582	CGGCTGGCGGATGCGCTGCAG
FUBP1	8880	broad.mit.edu;hgsc.bcm.edu	GRCh37	1	78422268	78422269	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T			TCGA-HT-7608-01	TCGA-HT-7608-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41	54			ENST00000370768.2:c.1693dupA	p.Thr565AsnfsTer2	p.T565Nfs*2	ENST00000370768	NM_003902.3	565	act/aAct	0	0.406	TTGTCCATTAGTTTGAGTTGTA
CIC	23152	broad.mit.edu	GRCh37	19	42792020	42792021	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-			TCGA-HT-7608-01	TCGA-HT-7608-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5	5			ENST00000575354.2:c.825_826delGA	p.Lys276ValfsTer38	p.K276Vfs*38	ENST00000575354	NM_015125.3	275	aAG/a	0	0.649	AAGGACCGAAAGAAGTCCAGCT
LRRC32	2615	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	76371010	76371010	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-P5-A5EW-01	TCGA-P5-A5EW-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73	14			ENST00000407242.2:c.1627C>T	p.Leu543=	p.L543=	ENST00000407242	NM_005512.2	543	Ctg/Ttg	0	0.637	TTGTTTCGCAGGTCCAGCACC
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	by1000genomes	TCGA-P5-A5EW-01	TCGA-P5-A5EW-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3	42			ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	0	0.542	GGCACAAACACGCACCTCAAA
KRI1	65095	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	10668901	10668901	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-P5-A5EW-01	TCGA-P5-A5EW-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79	23			ENST00000312962.6:c.1227C>T	p.Asp409=	p.D409=	ENST00000312962	NM_023008.3	409	gaC/gaT	0	0.602	CGTAGTACTCGTCCCCAAAGC
CCDC105	126402	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	15133702	15133702	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-P5-A5EW-01	TCGA-P5-A5EW-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	16	9			ENST00000292574.3:c.1271G>T	p.Cys424Phe	p.C424F	ENST00000292574	NM_173482.2	424	tGc/tTc	0	0.617	AAGCTGCAGTGCCACATCACG
TMCC2	9911	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	205210633	205210633	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G			TCGA-P5-A5EW-01	TCGA-P5-A5EW-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	38	40			ENST00000358024.3:c.208A>G	p.Lys70Glu	p.K70E	ENST00000358024	NM_014858.3	70	Aaa/Gaa	0	0.557	CCCCCTTAAGAAAATCCAGCA
OR2B11	127623	hgsc.bcm.edu;broad.mit.edu	GRCh37	1	247614765	247614765	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-P5-A5EW-01	TCGA-P5-A5EW-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	54	4			ENST00000318749.6:c.520G>A	p.Gly174Arg	p.G174R	ENST00000318749	NM_001004492.1	174	Ggg/Agg	0	0.597	ACCTGCCGCCCGCAGAATGGC
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-P5-A5EW-01	TCGA-P5-A5EW-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	31	26			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
CDCP1	64866	hgsc.bcm.edu;broad.mit.edu	GRCh37	3	45127212	45127212	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-P5-A5EW-01	TCGA-P5-A5EW-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	144	12			ENST00000296129.1:c.2429A>G	p.His810Arg	p.H810R	ENST00000296129	NM_022842.4	810	cAt/cGt	0	0.552	ATTGTTGGGATGGGAGAAGGT
PCDHGA1	56114	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	140711256	140711256	+	synonymous_variant	Silent	SNP	C	C	A			TCGA-P5-A5EW-01	TCGA-P5-A5EW-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62	35			ENST00000517417.1:c.1005C>A	p.Ile335=	p.I335=	ENST00000517417	NM_018912.2	335	atC/atA	0	0.418	AGGTACTGATCAAAGTTTTGG
GABRP	2568	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	170236583	170236583	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-P5-A5EW-01	TCGA-P5-A5EW-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91	83			ENST00000518525.1:c.844G>A	p.Val282Met	p.V282M	ENST00000518525		282	Gtg/Atg	0	0.517	AGTGACGACCGTGTTATCAAT
FBXL6	26233	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	145580132	145580132	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-P5-A5EW-01	TCGA-P5-A5EW-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61	59			ENST00000331890.5:c.1053C>T	p.Pro351=	p.P351=	ENST00000331890	NM_012162.3	351	ccC/ccT	0	0.652	AGCCTGGTCCGGGAGCCACCC
OPHN1	4983	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	67413796	67413796	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C			TCGA-P5-A5EW-01	TCGA-P5-A5EW-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	34	15			ENST00000355520.5:c.1139-2A>G		p.X380_splice	ENST00000355520	NM_002547.2			0	0.408	TTAGCTCCACTGTTTCAAGCA
RGPD3	653489	broad.mit.edu;ucsc.edu	GRCh37	2	107029596	107029596	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-P5-A5EW-01	TCGA-P5-A5EW-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9	81			ENST00000409886.3:c.5210A>G	p.Asn1737Ser	p.N1737S	ENST00000409886	NM_001144013.1	1737	aAt/aGt	0	0.438	CAACATCGTATTTATAACAGG
CYP39A1	51302	broad.mit.edu;ucsc.edu	GRCh37	6	46518143	46518143	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-P5-A5EW-01	TCGA-P5-A5EW-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42	19			ENST00000275016.2:c.1370C>T	p.Pro457Leu	p.P457L	ENST00000275016	NM_001278739.1	457	cCg/cTg	0	0.458	TTGCCCTTCCGGCTGGGGGAC
ATRX	546	broad.mit.edu;hgsc.bcm.edu	GRCh37	X	76939758	76939762	+	frameshift_variant	Frame_Shift_Del	DEL	TTTCT	TTTCT	-			TCGA-P5-A5EW-01	TCGA-P5-A5EW-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37	23			ENST00000373344.5:c.986_990delAGAAA	p.Lys329IlefsTer3	p.K329Ifs*3	ENST00000373344	NM_000489.3	329	aAGAAA/a	0	0.341	AATCATCTAATTTCTTTTCTTCTCC
MAGEA6	4105	broad.mit.edu;hgsc.bcm.edu	GRCh37	X	151870011	151870011	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-			TCGA-P5-A5EW-01	TCGA-P5-A5EW-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	219	144			ENST00000329342.5:c.703delG	p.Glu235LysfsTer50	p.E235Kfs*50	ENST00000329342	NM_005363.2	234	aGg/ag	0	0.532	TTTGAGGGGAGGGAAGACAGT
ADARB2	105	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	1779285	1779285	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	328	55			ENST00000381312.1:c.60C>G	p.Cys20Trp	p.C20W	ENST00000381312	NM_018702.3	20	tgC/tgG	0	0.701	TCTTGGACTTGCATTTGAGTT
SLC17A6	57084	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	22360149	22360149	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	31	9			ENST00000263160.3:c.70C>G	p.Leu24Val	p.L24V	ENST00000263160	NM_020346.2	24	Ctc/Gtc	0	0.473	TGGAAAATCACTCGGCCAGAT
OR5D14	219436	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	55563737	55563737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145440752	byFrequency	TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	63	35			ENST00000335605.1:c.706C>T	p.Arg236Cys	p.R236C	ENST00000335605	NM_001004735.1	236	Cgc/Tgc	0	0.463	TGTTAGTGGGCGCCACAAAGC
MMP20	9313	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	102465488	102465488	+	splice_region_variant,synonymous_variant	Splice_Region	SNP	C	C	G			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24	16			ENST00000260228.2:c.954G>C	p.Arg318=	p.R318=	ENST00000260228	NM_004771.3	318	cgG/cgC	0	0.418	TCCAGAAAATCCTATGGGACA
MDM2	4193	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	69230521	69230521	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52	28			ENST00000462284.1:c.910T>C	p.Ser304Pro	p.S304P	ENST00000462284	NM_002392.5	304	Tcc/Ccc	0	0.308	TCCTGAAATTTCCTTAGCTGT
GALC	2581	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	14	88454494	88454494	+	missense_variant	Missense_Mutation	SNP	T	T	A			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41	18			ENST00000261304.2:c.322A>T	p.Thr108Ser	p.T108S	ENST00000261304	NM_000153.3	108	Aca/Tca	0	0.358	CTACCTGTTGTCTGCCCATCA
LIPC	3990	hgsc.bcm.edu;broad.mit.edu	GRCh37	15	58855814	58855814	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95	7			ENST00000356113.6:c.1280C>T	p.Ala427Val	p.A427V	ENST00000356113		427	gCc/gTc	0	0.507	GCAGTGTGGGCCAATGTCTGG
LINS	55180	hgsc.bcm.edu;broad.mit.edu	GRCh37	15	101109585	101109585	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs148450316		TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	100	6			ENST00000314742.8:c.2132G>C	p.Arg711Thr	p.R711T	ENST00000314742	NM_001040616.2	711	aGa/aCa	0	0.383	TTTTACTATTCTGTAAAATAT
ANKRD11	29123	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	89351668	89351668	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	147	11			ENST00000301030.4:c.1282C>G	p.Leu428Val	p.L428V	ENST00000301030	NM_001256183.1	428	Ctc/Gtc	0	0.488	TGTGCCGAGAGTCTCAGCTTC
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33	28			ENST00000269305.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ttg	0	0.537	GGCACCACCACACTATGTCGA
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	T			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	56	38			ENST00000269305.4:c.584T>A	p.Ile195Asn	p.I195N	ENST00000269305	NM_001126112.2	195	aTc/aAc	0	0.552	TTCCACTCGGATAAGATGCTG
EFCAB5	374786	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	28409944	28409944	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	206	34			ENST00000394835.3:c.3462C>T	p.Tyr1154=	p.Y1154=	ENST00000394835	NM_198529.3	1154	taC/taT	0	0.398	CCTATCACTACGTCCACAGCC
CCL11	6356	hgsc.bcm.edu;broad.mit.edu	GRCh37	17	32612839	32612839	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	248	14			ENST00000305869.3:c.12C>T	p.Ser4=	p.S4=	ENST00000305869	NM_002986.2	4	tcC/tcT	0	0.597	TGAAGGTCTCCGCAGCACTTC
LAMA1	284217	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	18	7023260	7023260	+	synonymous_variant	Silent	SNP	C	C	A			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	43	34			ENST00000389658.3:c.2604G>T	p.Gly868=	p.G868=	ENST00000389658	NM_005559.3	868	ggG/ggT	0	0.602	TCAGGCACTCCCCGGTGACTG
STARD6	147323	hgsc.bcm.edu;broad.mit.edu	GRCh37	18	51858176	51858176	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	70	4			ENST00000581310.1:c.321C>T	p.Ser107=	p.S107=	ENST00000581310		107	tcC/tcT	0	0.368	AGTCTCGAGGGGAAATGGAGC
TSHZ1	10194	hgsc.bcm.edu;broad.mit.edu	GRCh37	18	72999933	72999933	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	63	4			ENST00000322038.5:c.2436G>A	p.Thr812=	p.T812=	ENST00000322038	NM_005786.5	812	acG/acA	0	0.602	AGTCCTCCACGCCCTCCACAG
CSNK1G2	1455	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	1979554	1979554	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52	42			ENST00000255641.8:c.914A>G	p.Tyr305Cys	p.Y305C	ENST00000255641	NM_001319.6	305	tAt/tGt	0	0.652	AAGCCCGACTATGACTACCTG
ICAM1	3383	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	10394873	10394873	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	50	30			ENST00000264832.3:c.802G>A	p.Asp268Asn	p.D268N	ENST00000264832	NM_000201.2	268	Gac/Aac	0	0.632	CTATGGCAACGACTCCTTCTC
AKAP8	10270	hgsc.bcm.edu;broad.mit.edu	GRCh37	19	15472624	15472624	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	34	3			ENST00000269701.2:c.1312G>C	p.Val438Leu	p.V438L	ENST00000269701	NM_005858.3	438	Gta/Cta	0	0.458	TTTCTGTTTACAATGTATTCC
ADCK4	79934	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	41197999	41197999	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	25	18			ENST00000324464.3:c.1576G>C	p.Asp526His	p.D526H	ENST00000324464	NM_024876.3	526	Gac/Cac	0	0.672	GTGGCTGCGTCTGGCTGGCGA
ZNF460	10794	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	57802257	57802257	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	65	38			ENST00000360338.3:c.348G>C	p.Glu116Asp	p.E116D	ENST00000360338	NM_006635.3	116	gaG/gaC	0	0.473	CACAGAGTGAGAAACTCCATG
TCHH	7062	hgsc.bcm.edu;broad.mit.edu	GRCh37	1	152084077	152084077	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	290	17			ENST00000368804.1:c.1616G>C	p.Arg539Thr	p.R539T	ENST00000368804	NM_007113.3	539	aGa/aCa	0	0.652	CTGCTCGCGTCTTAGTTGTTG
LAMC1	3915	hgsc.bcm.edu;broad.mit.edu	GRCh37	1	183086809	183086809	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91	5			ENST00000258341.4:c.1828G>A	p.Ala610Thr	p.A610T	ENST00000258341	NM_002293.3	610	Gct/Act	0	0.483	ACCCTTGATCGCTCAGGGCAA
MIA3	375056	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	222803484	222803484	+	synonymous_variant	Silent	SNP	C	C	G			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28	21			ENST00000344922.5:c.2922C>G	p.Val974=	p.V974=	ENST00000344922	NM_198551.2	974	gtC/gtG	0	0.428	TGGAAAAAGTCCTAGATAAGG
MYH7B	57644	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	20	33567544	33567544	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90	54			ENST00000262873.7:c.405G>A	p.Thr135=	p.T135=	ENST00000262873	NM_020884.3	135	acG/acA	0	0.637	CCATGATGACGCACCTGAACG
KCNB1	3745	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	20	48098819	48098819	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	51	7			ENST00000371741.4:c.199G>C	p.Asp67His	p.D67H	ENST00000371741	NM_004975.2	67	Gac/Cac	0	0.662	AGCAGCGAGTCGTGCGTGTTG
APOB	338	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	21228306	21228306	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91	77			ENST00000233242.1:c.11434G>C	p.Glu3812Gln	p.E3812Q	ENST00000233242	NM_000384.2	3812	Gag/Cag	0	0.423	ACGGTTATCTCAAAAAAGGGA
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499		TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	50	32			ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	0	0.398	TAAGCATGACGACCTATGATG
VHL	7428	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	10191622	10191622	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	19	16			ENST00000256474.2:c.615C>T	p.Arg205=	p.R205=	ENST00000256474	NM_000551.3	205	cgC/cgT	0	0.468	CACAGGAGCGCATTGCACATC
MED23	9439	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	131929091	131929091	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23	17			ENST00000368068.3:c.1198G>A	p.Asp400Asn	p.D400N	ENST00000368068	NM_004830.3	400	Gac/Aac	0	0.343	TATAGCAAGTCGAAGAGCTTC
RBAK	57786	hgsc.bcm.edu;ucsc.edu	GRCh37	7	5104674	5104674	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61	22			ENST00000396912.1:c.1587C>G	p.His529Gln	p.H529Q	ENST00000396912	NM_021163.3	529	caC/caG	0	0.383	TCGATGGGCACCAGCCACTTC
HEPACAM2	253012	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	92838050	92838050	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24	32			ENST00000394468.2:c.855G>C	p.Arg285Ser	p.R285S	ENST00000394468	NM_001039372.1	285	agG/agC	0	0.443	TATTGTCAGTCCTCCTAATCC
KIAA1429	25962	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	95530133	95530133	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	16	12			ENST00000297591.5:c.2551G>A	p.Ala851Thr	p.A851T	ENST00000297591	NM_015496.4	851	Gca/Aca	0	0.318	AGTATGCATGCGTAATTATAA
SVEP1	79987	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	113139603	113139603	+	synonymous_variant	Silent	SNP	G	G	C			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79	35			ENST00000401783.2:c.10452C>G	p.Arg3484=	p.R3484=	ENST00000401783	NM_153366.3	3484	cgC/cgG	0	0.502	AAGCATTTGGGCGTTGGCAGA
CACNA1B	774	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	140946550	140946550	+	synonymous_variant	Silent	SNP	C	C	G			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17	9			ENST00000371372.1:c.3717C>G	p.Ser1239=	p.S1239=	ENST00000371372	NM_001243812.1	1239	tcC/tcG	0	0.582	CTAGAGGATCCAAAGGGAAAG
AMPD1	270	broad.mit.edu;ucsc.edu	GRCh37	1	115216305	115216305	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42	40			ENST00000520113.2:c.2139C>T	p.Cys713=	p.C713=	ENST00000520113		713	tgC/tgT	0	0.438	TTGCCACTTCGCACATATCAC
FRMD7	90167	broad.mit.edu;ucsc.edu	GRCh37	X	131214292	131214292	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	13	3			ENST00000298542.4:c.908G>C	p.Gly303Ala	p.G303A	ENST00000298542	NM_194277.2	303	gGa/gCa	0	0.373	TTGGGTTCGTCCACTATCATA
MMP24	10893	broad.mit.edu;ucsc.edu	GRCh37	20	33862232	33862232	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	135	90			ENST00000246186.6:c.1758C>T	p.Asp586=	p.D586=	ENST00000246186	NM_006690.3	586	gaC/gaT	0	0.657	CCCAGGACGACGTGGACATCA
GABRG2	2566	broad.mit.edu;ucsc.edu	GRCh37	5	161569181	161569181	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	92	36			ENST00000414552.2:c.901G>T	p.Val301Phe	p.V301F	ENST00000414552	NM_198903.2	301	Gtc/Ttc	0	0.403	AGATTATGTGGTCATGTCTGT
TFPT	29844	broad.mit.edu;hgsc.bcm.edu	GRCh37	19	54611378	54611379	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCATC			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	152	30			ENST00000391759.1:c.592_596dupGATGG	p.Arg200MetfsTer9	p.R200Mfs*9	ENST00000391759	NM_013342.3	199	gga/ggGATGGa	0	0.713	CTGCTCGGCGTCCATCCCGTGG
ATRX	546	broad.mit.edu;hgsc.bcm.edu	GRCh37	X	76939914	76939915	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-			TCGA-FG-8185-01	TCGA-FG-8185-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21	70			ENST00000373344.5:c.833_834delCT	p.Thr278SerfsTer3	p.T278Sfs*3	ENST00000373344	NM_000489.3	278	aCT/a	0	0.371	TGTTACATGCAGTGACCAAGTC
MYO3A	53904	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	26463288	26463288	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	118	21			ENST00000265944.5:c.4095G>T	p.Gln1365His	p.Q1365H	ENST00000265944	NM_017433.4	1365	caG/caT	0	0.438	GAAGGCAGCAGTTGAGGAAGG
CYP2C19	1557	hgsc.bcm.edu;broad.mit.edu	GRCh37	10	96535297	96535297	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs77576043		TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184	11			ENST00000371321.3:c.481+1G>C		p.X161_splice	ENST00000371321	NM_000769.1			0	0.498	AAAACCAAGGGTGGGTGAACA
WDR96	80217	hgsc.bcm.edu;broad.mit.edu	GRCh37	10	105990460	105990460	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	87	5			ENST00000357060.3:c.207C>T	p.Gly69=	p.G69=	ENST00000357060	NM_025145.5	69	ggC/ggT	0	0.408	TTGCCATGACGCCCACAATTC
DCHS1	8642	hgsc.bcm.edu;broad.mit.edu	GRCh37	11	6645159	6645159	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	185	10			ENST00000299441.3:c.7748G>C	p.Ser2583Thr	p.S2583T	ENST00000299441	NM_003737.2	2583	aGc/aCc	0	0.537	CACGACTGAGCTTTGGGGTGG
DCHS1	8642	hgsc.bcm.edu;broad.mit.edu	GRCh37	11	6645181	6645181	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	119	6			ENST00000299441.3:c.7726G>C	p.Asp2576His	p.D2576H	ENST00000299441	NM_003737.2	2576	Gac/Cac	0	0.562	TGCCCACGGTCAGCTGCAGCC
RPUSD4	84881	hgsc.bcm.edu;broad.mit.edu	GRCh37	11	126075477	126075477	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143531642		TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	121	9			ENST00000298317.4:c.682G>A	p.Asp228Asn	p.D228N	ENST00000298317	NM_032795.2	228	Gat/Aat	0	0.557	ATTTTCCCATCGTCCATGCGG
CUL4A	8451	hgsc.bcm.edu;broad.mit.edu	GRCh37	13	113891149	113891149	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	70	4			ENST00000375440.4:c.861T>C	p.Ile287=	p.I287=	ENST00000375440	NM_001008895.2	287	atT/atC	0	0.358	AACCACTGATTGCTTGTGTGG
SUPT16H	11198	hgsc.bcm.edu;broad.mit.edu	GRCh37	14	21838616	21838616	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62	4			ENST00000216297.2:c.362T>C	p.Met121Thr	p.M121T	ENST00000216297	NM_007192.3	121	aTg/aCg	0	0.383	GGCTTCAATCATTTTGTCAAA
CHD8	57680	hgsc.bcm.edu;broad.mit.edu	GRCh37	14	21861840	21861840	+	synonymous_variant	Silent	SNP	T	T	G			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	60	5			ENST00000399982.2:c.6114A>C	p.Pro2038=	p.P2038=	ENST00000399982	NM_001170629.1	2038	ccA/ccC	0	0.547	CATAGTCTTGTGGGGTTGGTC
TRIM9	114088	hgsc.bcm.edu;broad.mit.edu	GRCh37	14	51446210	51446210	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	222	13			ENST00000298355.3:c.1965A>G	p.Arg655=	p.R655=	ENST00000298355	NM_015163.5	655	agA/agG	0	0.453	TCAAGTTTTTTCTATTTAAGT
GATM	2628	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	45658331	45658331	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68	23			ENST00000396659.3:c.891A>G	p.Lys297=	p.K297=	ENST00000396659	NM_001482.2	297	aaA/aaG	0	0.428	GATTGGGATCTTTAAAGGAGA
SEMA6D	80031	hgsc.bcm.edu;broad.mit.edu	GRCh37	15	48052514	48052514	+	stop_gained	Nonsense_Mutation	SNP	T	T	A			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	59	3			ENST00000316364.5:c.123T>A	p.Tyr41Ter	p.Y41*	ENST00000316364	NM_153618.1	41	taT/taA	0	0.418	CAAGGCAATATCCGGTTTTTA
PDE8A	5151	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	85619979	85619979	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	150	14			ENST00000310298.4:c.507G>C	p.Glu169Asp	p.E169D	ENST00000310298		169	gaG/gaC	0	0.294	ATAGAGAAGAGTTGTCCGTAA
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	50	65			ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	0	0.642	GCAGCGCTCATGGTGGGGGCA
ZNF207	7756	hgsc.bcm.edu;broad.mit.edu	GRCh37	17	30696691	30696691	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	65	7			ENST00000394670.4:c.1398G>A	p.Pro466=	p.P466=	ENST00000394670	NM_001098507.1	466	ccG/ccA	0	0.527	GGCAGGGACCGCCAATGGTGC
CCR7	1236	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	38715155	38715155	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61	7			ENST00000246657.2:c.50T>C	p.Val17Ala	p.V17A	ENST00000246657	NM_001838.3	17	gTc/gCc	0	0.498	CTGGAAAATGACAAGGAGAGC
C17orf47	5414	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	56620229	56620229	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	89	48			ENST00000321691.3:c.1319G>A	p.Ser440Asn	p.S440N	ENST00000321691	NM_001038704.2	440	aGc/aAc	0	0.507	TGTCAGCTGGCTTTGGGGTGT
ABCA6	23460	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	67080574	67080574	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	387	159			ENST00000284425.2:c.4259A>G	p.Lys1420Arg	p.K1420R	ENST00000284425	NM_080284.2	1420	aAg/aGg	0	0.453	CGCACGTACCTTTCTCGTGAT
SLC26A11	284129	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	78199637	78199637	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	163	26			ENST00000361193.3:c.515A>G	p.Asn172Ser	p.N172S	ENST00000361193	NM_001166347.1	172	aAc/aGc	0	0.587	TTTGGACAGAACCTGCTGGGA
ASXL3	80816	hgsc.bcm.edu;broad.mit.edu	GRCh37	18	31325552	31325552	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	116	5			ENST00000269197.5:c.5740G>C	p.Asp1914His	p.D1914H	ENST00000269197	NM_030632.1	1914	Gac/Cac	0	0.532	ATTTCATGTTGACAAGAATGG
MC4R	4160	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	18	58038877	58038877	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61	11			ENST00000299766.3:c.706C>T	p.Arg236Cys	p.R236C	ENST00000299766	NM_005912.2	236	Cgc/Tgc	0	0.517	GCACCTTGGCGGATGGCACCA
KRI1	65095	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	10671046	10671046	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57	7			ENST00000312962.6:c.760C>T	p.Arg254Cys	p.R254C	ENST00000312962	NM_023008.3	254	Cgc/Tgc	0	0.552	tcctcATAGCGTTTGTTGAGG
CYP4F22	126410	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	15651449	15651449	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146265982		TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	80	25			ENST00000269703.3:c.860G>A	p.Arg287His	p.R287H	ENST00000269703	NM_173483.3	287	cGt/cAt	0	0.632	CGGGCACTGCGTCAGCAGGGG
NPHS1	4868	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	36340183	36340183	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	31	14			ENST00000378910.5:c.795C>T	p.Cys265=	p.C265=	ENST00000378910	NM_004646.3	265	tgC/tgT	0	0.657	CTCGGGCCACGCACGGCAGCT
SIPA1L3	23094	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	38643516	38643516	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	202	47			ENST00000222345.6:c.3570T>C	p.Asp1190=	p.D1190=	ENST00000222345	NM_015073.1	1190	gaT/gaC	0	0.617	TATCTCTTGATCCCCACTTCA
ZNF17	7565	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	57932608	57932608	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36	10			ENST00000601808.1:c.1748A>G	p.Lys583Arg	p.K583R	ENST00000601808	NM_006959.2	583	aAa/aGa	0	0.428	AGAACTTACAAATGCAGCAAA
TAS1R2	80834	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	19181078	19181078	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	54	15			ENST00000375371.3:c.886G>A	p.Ala296Thr	p.A296T	ENST00000375371	NM_152232.2	296	Gcc/Acc	0	0.637	ATCCACACGGCGCCAGTGAAG
SNRNP40	9410	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	31744294	31744294	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	63	7			ENST00000263694.4:c.707A>G	p.Asp236Gly	p.D236G	ENST00000263694	NM_004814.2	236	gAt/gGt	0	0.448	AGTCACTGAATCTGCATGGCC
RLF	6018	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	40702367	40702367	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	111	51			ENST00000372771.4:c.1993C>G	p.Leu665Val	p.L665V	ENST00000372771	NM_012421.3	665	Ctg/Gtg	0	0.418	AGATTGCCACCTGCAAGACAG
AGL	178	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	100353559	100353559	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57	6			ENST00000294724.4:c.2707G>A	p.Glu903Lys	p.E903K	ENST00000294724	NM_000028.2	903	Gag/Aag	0	0.373	AACTTTGGCTGAGCTAAATCA
SYCP1	6847	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	115487052	115487052	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	31	4			ENST00000369522.3:c.2019A>G	p.Ile673Met	p.I673M	ENST00000369522	NM_003176.2	673	atA/atG	0	0.279	ACAAAAAGATATCAGAAGAAA
CD1E	913	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	158325321	158325321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142840776		TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	48	7			ENST00000368167.3:c.587G>A	p.Gly196Glu	p.G196E	ENST00000368167	NM_030893.3	196	gGg/gAg	0	0.473	TTTCTAGCGGGGCTCATGGAA
SCYL3	57147	hgsc.bcm.edu;broad.mit.edu	GRCh37	1	169823532	169823532	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	121	7			ENST00000367772.4:c.2048T>C	p.Ile683Thr	p.I683T	ENST00000367772	NM_181093.3	683	aTt/aCt	0	0.393	AGAAGGCTTAATTTCTGGGAT
MROH9	80133	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	170928725	170928725	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	55	8			ENST00000367759.4:c.275T>C	p.Ile92Thr	p.I92T	ENST00000367759	NM_001163629.1	92	aTt/aCt	0	0.363	TATGAGTACATTGAGGACATG
OR2M7	391196	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	248486965	248486965	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71	8			ENST00000317965.2:c.906G>T	p.Met302Ile	p.M302I	ENST00000317965	NM_001004691.1	302	atG/atT	0	0.403	CTAAGATTTTCATTAATGCTC
TGM6	343641	hgsc.bcm.edu;broad.mit.edu	GRCh37	20	2411182	2411182	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	63	4			ENST00000202625.2:c.1769T>C	p.Val590Ala	p.V590A	ENST00000202625	NM_198994.2	590	gTc/gCc	0	0.458	ATGTGCCTTGTCACCAAAGGA
TPX2	22974	hgsc.bcm.edu;broad.mit.edu	GRCh37	20	30388772	30388772	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	166	10			ENST00000300403.6:c.2134-1G>C		p.X712_splice	ENST00000300403	NM_012112.4			0	0.398	TTACTTTGCAGGTGCATAAGG
EIF2AK3	9451	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	88913303	88913303	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	137	10			ENST00000303236.3:c.377A>G	p.Lys126Arg	p.K126R	ENST00000303236	NM_004836.5	126	aAg/aGg	0	0.353	ATCCCACTGCTTTTTACCATG
PTPN4	5775	hgsc.bcm.edu;broad.mit.edu	GRCh37	2	120709680	120709680	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	117	7			ENST00000263708.2:c.1788A>G	p.Glu596=	p.E596=	ENST00000263708	NM_002830.3	596	gaA/gaG	0	0.403	ATTCTGGGGAACTCATGCTTC
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	179463964	179463964	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	137	29			ENST00000589042.1:c.56556C>T	p.Gly18852=	p.G18852=	ENST00000589042	NM_001267550.1	18852	ggC/ggT	0	0.428	CATATTCATGGCCTTCTAGCA
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73	26			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
NEK4	6787	hgsc.bcm.edu;broad.mit.edu	GRCh37	3	52802575	52802575	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	127	7			ENST00000233027.5:c.139C>T	p.Arg47Trp	p.R47W	ENST00000233027	NM_001193533.1	47	Cgg/Tgg	0	0.453	GCAGCTCGCCGCTCTCGGCTA
CWH43	80157	hgsc.bcm.edu;broad.mit.edu	GRCh37	4	49000535	49000535	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	152	11			ENST00000226432.4:c.772C>G	p.Arg258Gly	p.R258G	ENST00000226432	NM_025087.2	258	Cgt/Ggt	0	0.443	TTTGTGGTTTCGTGGTACTGG
KDR	3791	hgsc.bcm.edu;broad.mit.edu	GRCh37	4	55981079	55981079	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58	4			ENST00000263923.4:c.620A>G	p.Glu207Gly	p.E207G	ENST00000263923	NM_002253.2	207	gAa/gGa	0	0.373	CTGGTAACTTTCATCATTAAT
DNAH5	1767	hgsc.bcm.edu;broad.mit.edu	GRCh37	5	13792273	13792273	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	70	4			ENST00000265104.4:c.8278A>G	p.Arg2760Gly	p.R2760G	ENST00000265104	NM_001369.2	2760	Aga/Gga	0	0.423	ACAGAATCTCTCACTTCTTCT
PDZD2	23037	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	32090257	32090257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147353592		TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	491	48			ENST00000438447.1:c.6703C>T	p.Arg2235Trp	p.R2235W	ENST00000438447		2235	Cgg/Tgg	0	0.632	CCATTTTGGACGGGAGGGTCA
MAP1B	4131	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	71493611	71493611	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36	16			ENST00000296755.7:c.4429A>G	p.Lys1477Glu	p.K1477E	ENST00000296755	NM_005909.3	1477	Aaa/Gaa	0	0.403	CCAAGAAAAGAAAACTGATGA
AQPEP	206338	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	115298645	115298645	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97	24			ENST00000357872.4:c.331C>T	p.Leu111=	p.L111=	ENST00000357872	NM_173800.4	111	Ctg/Ttg	0	0.701	CGATCTGGAGCTGTGGCCGCA
FOXQ1	94234	hgsc.bcm.edu;broad.mit.edu	GRCh37	6	1313391	1313391	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78	4			ENST00000296839.2:c.452G>A	p.Gly151Asp	p.G151D	ENST00000296839	NM_033260.3	151	gGc/gAc	0	0.652	TACCTCATGGGCAAGTTCCCC
TREML2	79865	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	41160191	41160191	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	46	7			ENST00000483722.1:c.940C>T	p.Pro314Ser	p.P314S	ENST00000483722	NM_024807.2	314	Ccc/Tcc	0	0.587	TCCACATAGGGCTCTGGTCTT
PRDM1	639	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	106553291	106553291	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	65	10			ENST00000369096.4:c.1256G>A	p.Gly419Asp	p.G419D	ENST00000369096	NM_001198.3	419	gGc/gAc	0	0.587	CCCCCCTACGGCATGAATTGT
IL6	3569	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	22769188	22769188	+	missense_variant	Missense_Mutation	SNP	A	A	T			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	72	11			ENST00000404625.1:c.380A>T	p.Glu127Val	p.E127V	ENST00000404625		127	gAg/gTg	0	0.458	GTATACCTAGAGTACCTCCAG
GRB10	2887	hgsc.bcm.edu;broad.mit.edu	GRCh37	7	50686969	50686969	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	123	6			ENST00000398812.2:c.675A>G	p.Glu225=	p.E225=	ENST00000398812	NM_005311.4	225	gaA/gaG	0	0.443	GCTCATGGTCTTCCAAGCACC
INTS9	55756	hgsc.bcm.edu;broad.mit.edu	GRCh37	8	28625815	28625815	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	196	11			ENST00000521022.1:c.1825G>C	p.Glu609Gln	p.E609Q	ENST00000521022	NM_018250.3	609	Gag/Cag	0	0.502	GCTGTGTCCTCCACCTTAATA
TG	7038	hgsc.bcm.edu;broad.mit.edu	GRCh37	8	133912511	133912511	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58	5			ENST00000220616.4:c.3360G>A	p.Ser1120=	p.S1120=	ENST00000220616	NM_003235.4	1120	tcG/tcA	0	0.622	TGCAGGCATCGGGGGCTGGCA
RORB	6096	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	77257632	77257632	+	stop_gained	Nonsense_Mutation	SNP	C	C	T			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68	11			ENST00000376896.3:c.538C>T	p.Gln180Ter	p.Q180*	ENST00000376896	NM_006914.3	180	Caa/Taa	0	0.468	ACAGATAAAGCAAGAACCTAT
MSL3	10943	hgsc.bcm.edu;ucsc.edu	GRCh37	X	11783854	11783854	+	splice_region_variant,intron_variant	Splice_Region	SNP	T	T	C			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	136	25			ENST00000312196.4:c.1171+6T>C		p.X391_splice	ENST00000312196	NM_078629.3			0	0.587	AAAGAGTAGGTTCATTCTCGG
FMR1NB	158521	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	147084823	147084823	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23	7			ENST00000370467.3:c.380A>G	p.Asn127Ser	p.N127S	ENST00000370467	NM_152578.2	127	aAt/aGt	0	0.373	GCTTTGCTGAATTTTTTCTTT
UTY	7404	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	Y	15522901	15522901	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37	22			ENST00000331397.4:c.527T>C	p.Val176Ala	p.V176A	ENST00000331397	NM_001258267.1	176	gTg/gCg	0	0.413	GTCTGTGTTCACTTTGAACAT
TMEM175	84286	broad.mit.edu;ucsc.edu	GRCh37	4	944293	944293	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	106	11			ENST00000264771.4:c.277G>C	p.Ala93Pro	p.A93P	ENST00000264771	NM_032326.2	93	Gca/Cca	0	0.597	AGTGGCCTGGGCAGCACACAC
MKI67	4288	broad.mit.edu;ucsc.edu	GRCh37	10	129923863	129923863	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	122	14			ENST00000368654.3:c.69C>G	p.Ser23Arg	p.S23R	ENST00000368654	NM_002417.4	23	agC/agG	0	0.517	AGGTGCTGAGGCTCAGGGGAA
MBL2	4153	broad.mit.edu;ucsc.edu	GRCh37	10	54531233	54531233	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93	11			ENST00000373968.3:c.163A>G	p.Thr55Ala	p.T55A	ENST00000373968	NM_000242.2	55	Acc/Gcc	0	0.537	TCTCCCTTGGTGCCATCACGC
HOXC4	3221	broad.mit.edu;ucsc.edu	GRCh37	12	54447735	54447735	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76	10			ENST00000430889.2:c.29C>G	p.Ser10Cys	p.S10C	ENST00000430889	NM_153633.2	10	tCt/tGt	0	0.423	TTGATGGACTCTAACTACATC
ARID1A	8289	broad.mit.edu;hgsc.bcm.edu	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	129	23			ENST00000324856.7:c.3977delC	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	0	0.597	CTAGCCGCTACCCCCCgcagc
CAD	790	broad.mit.edu;hgsc.bcm.edu	GRCh37	2	27462334	27462334	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69	25			ENST00000264705.4:c.5391delG	p.Gln1798ArgfsTer33	p.Q1798Rfs*33	ENST00000264705	NM_004341.3	1797	Ggg/gg	0	0.567	CTATATCGATGGGCAGGTACG
FBN2	2201	broad.mit.edu;hgsc.bcm.edu	GRCh37	5	127782200	127782203	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75	16			ENST00000508053.1:c.923_926delAACA	p.Lys308ArgfsTer42	p.K308Rfs*42	ENST00000508053		308	aAACAg/ag	0	0.426	AGTTTCACTCTGTTTGTGACCAGC
EPB41L2	2037	broad.mit.edu;hgsc.bcm.edu	GRCh37	6	131229973	131229976	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	38	16			ENST00000337057.3:c.838_841delAAGA	p.Lys280AspfsTer3	p.K280Dfs*3	ENST00000337057	NM_001431.3	280	AAGAga/ga	0	0.284	CTCAGTTGTCTCTTTATTTCTTTA
NCOA4	8031	broad.mit.edu;hgsc.bcm.edu	GRCh37	10	51585027	51585029	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	22	13			ENST00000452682.1:c.1176_1178delGAA	p.Lys393del	p.K393del	ENST00000452682	NM_001145260.1	392	AAG/-	0	0.522	CTTGGAGGCCAAGAAACCATTGT
ARID5B	84159	broad.mit.edu;hgsc.bcm.edu	GRCh37	10	63845531	63845531	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91	58			ENST00000279873.7:c.1272delA	p.Lys424AsnfsTer55	p.K424Nfs*55	ENST00000279873	NM_032199.2	424	Aaa/aa	0	0.358	CAAACCTCGGAAACAGGAGAA
CDON	50937	broad.mit.edu;hgsc.bcm.edu	GRCh37	11	125891236	125891237	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73	19			ENST00000392693.3:c.255_256delTT	p.Leu87GlnfsTer15	p.L87Qfs*15	ENST00000392693	NM_001243597.1	85	ctTTct/ctct	0	0.475	GAGTTGAGAGAAAGAATTGTCA
PTPRR	5801	broad.mit.edu;hgsc.bcm.edu	GRCh37	12	71050530	71050532	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	159	43			ENST00000283228.2:c.1832_1834delAAG	p.Glu611del	p.E611del	ENST00000283228	NM_002849.3	611	gAAGga/gga	0	0.433	TCCACAACTCCTTCTTCTTTCAG
C14orf37	145407	broad.mit.edu;hgsc.bcm.edu	GRCh37	14	58605972	58605974	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	110	36			ENST00000267485.7:c.103_105delAGG	p.Arg35del	p.R35del	ENST00000267485	NM_001001872.2	35	AGG/-	0	0.478	GTGCTATCTCCCTCCTCCTTTCT
SMARCA4	6597	broad.mit.edu;hgsc.bcm.edu	GRCh37	19	11106926	11106928	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	145	29			ENST00000344626.4:c.1636_1638delAAG	p.Lys546del	p.K546del	ENST00000344626	NM_003072.3	544	cAGAag/cag	0	0.576	CTCATCGACCAGAAGAAGGACAA
ATRX	546	broad.mit.edu	GRCh37	X	76875860	76875861	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CA	CA	-			TCGA-HT-7688-01	TCGA-HT-7688-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	34	9			ENST00000373344.5:c.5272+2_5272+3delTG		p.X1758_splice	ENST00000373344	NM_000489.3			0	0.317	GATATTAACTCACACTCAATTA
ADARB2	105	hgsc.bcm.edu;broad.mit.edu	GRCh37	10	1405304	1405304	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7	10			ENST00000381312.1:c.996G>A	p.Ala332=	p.A332=	ENST00000381312	NM_018702.3	332	gcG/gcA	0	0.746	GTGCGGCCTGCGCGGCCTGAC
PRF1	5551	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	72358832	72358832	+	synonymous_variant	Silent	SNP	A	A	C			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	44	30			ENST00000441259.1:c.645T>G	p.Leu215=	p.L215=	ENST00000441259	NM_005041.4	215	ctT/ctG	0	0.662	AGTTGGAGATAAGCCTGAGGT
PDE6C	5146	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	95425134	95425134	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	34	9			ENST00000371447.3:c.2536G>A	p.Gly846Ser	p.G846S	ENST00000371447	NM_006204.3	846	Ggt/Agt	0	0.313	AGATTCAGGAGGTGGTGATGA
OR52B4	143496	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	4388941	4388941	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52	28			ENST00000408920.2:c.585A>G	p.Arg195=	p.R195=	ENST00000408920	NM_001005161.3	195	cgA/cgG	0	0.343	AAATGTTTATTCGAATGTCAT
SDS	10993	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	113830761	113830761	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	214	163			ENST00000257549.4:c.972T>C	p.Asn324=	p.N324=	ENST00000257549	NM_006843.2	324	aaT/aaC	0	0.617	TGGGCAACCTATTTGTCATGC
KLF5	688	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	13	73636332	73636332	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	44	46			ENST00000377687.4:c.595G>A	p.Ala199Thr	p.A199T	ENST00000377687	NM_001730.3	199	Gca/Aca	0	0.532	ACACCAGACCGCAGCTCCAGA
CLEC14A	161198	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	14	38723787	38723787	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	117	50			ENST00000342213.2:c.1441G>A	p.Ala481Thr	p.A481T	ENST00000342213	NM_175060.2	481	Gcg/Acg	0	0.547	GGGGACTCCGCCAGCAAGGCA
TELO2	9894	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	1557703	1557703	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30	15			ENST00000262319.6:c.2393G>A	p.Arg798Gln	p.R798Q	ENST00000262319	NM_016111.3	798	cGg/cAg	0	0.647	CTGGAAGCCCGGTCCTGGCTG
PDILT	204474	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	20387485	20387485	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs139247719		TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36	33			ENST00000302451.4:c.448C>T	p.Arg150Ter	p.R150*	ENST00000302451	NM_174924.1	150	Cga/Tga	0	0.463	CTAATTTGTCGTCTCAACCAA
ATXN2L	11273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	28847394	28847394	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	106	71			ENST00000395547.2:c.3036A>G	p.Ala1012=	p.A1012=	ENST00000395547	NM_148414.2	1012	gcA/gcG	0	0.687	GGGTGCCTGCACTCTCAGCTT
SEZ6L2	26470	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	29888271	29888271	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40	17			ENST00000308713.5:c.1910A>C	p.Glu637Ala	p.E637A	ENST00000308713	NM_001114099.2	637	gAg/gCg	0	0.667	CCTCGGGACCTCTGCAGGGGA
TSNAXIP1	55815	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	67859118	67859118	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	63	45			ENST00000388833.3:c.595G>A	p.Ala199Thr	p.A199T	ENST00000388833	NM_018430.2	199	Gca/Aca	0	0.542	GATCCTCATCGCAGACCTGAA
NEURL4	84461	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7231068	7231068	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98	69			ENST00000399464.2:c.418C>T	p.Arg140Cys	p.R140C	ENST00000399464	NM_032442.2	140	Cgc/Tgc	0	0.642	AACACAGAGCGTCCATCTCTC
PRKAR1A	5573	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	66526499	66526499	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74	55			ENST00000358598.2:c.1055G>A	p.Arg352Gln	p.R352Q	ENST00000358598	NM_212471.2	352	cGa/cAa	0	0.488	AAGCTGGACCGACCTAGATTT
SMCHD1	23347	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	18	2732375	2732375	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	53	33			ENST00000320876.6:c.3161A>G	p.His1054Arg	p.H1054R	ENST00000320876	NM_015295.2	1054	cAt/cGt	0	0.363	CAGATCAAACATCAGGATGAG
PRSS57	400668	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	691902	691902	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	48	21			ENST00000329267.7:c.337G>A	p.Asp113Asn	p.D113N	ENST00000329267	NM_214710.3	113	Gac/Aac	0	0.622	GGGTGGTAGTCGGGGTGTGTG
CIC	23152	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	42791817	42791817	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23	41			ENST00000575354.2:c.703G>T	p.Gly235Cys	p.G235C	ENST00000575354	NM_015125.3	235	Ggc/Tgc	0	0.612	CAAGATCCTGGGCGAGTGGTG
RBMXL1	494115	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	89448560	89448560	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	43	122			ENST00000399794.2:c.950G>A	p.Arg317His	p.R317H	ENST00000399794	NM_001162536.2	317	cGt/cAt	0	0.498	ATATCCATCACGTGAGCTGCT
DENND2D	79961	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	111738675	111738675	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7	32			ENST00000357640.4:c.508C>G	p.Leu170Val	p.L170V	ENST00000357640	NM_024901.4	170	Ctg/Gtg	0	0.552	ACTTCATCCAGGATCTGCAGG
OR6N2	81442	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	158746704	158746704	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	25	22			ENST00000339258.1:c.722G>A	p.Cys241Tyr	p.C241Y	ENST00000339258	NM_001005278.1	241	tGt/tAt	0	0.433	ATGTGAGGCACAGGTAGAAAA
EPRS	2058	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	220142262	220142262	+	synonymous_variant	Silent	SNP	T	T	A			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47	36			ENST00000366923.3:c.4425A>T	p.Gly1475=	p.G1475=	ENST00000366923	NM_004446.2	1475	ggA/ggT	0	0.433	GGCTTTTAGCTCCCATGGATG
TLR5	7100	hgsc.bcm.edu;ucsc.edu	GRCh37	1	223286129	223286129	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs764535	byFrequency	TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	55	35			ENST00000540964.1:c.245C>A	p.Thr82Asn	p.T82N	ENST00000540964		82	aCc/aAc	0	0.498	AGTCAAGGGGGTATACTGGCT
MMP9	4318	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	20	44641108	44641108	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	56	37			ENST00000372330.3:c.1217C>T	p.Ala406Val	p.A406V	ENST00000372330	NM_004994.2	406	gCg/gTg	0	0.637	TTCGGCCACGCGCTGGGCTTA
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36	25			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
ZBTB11	27107	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	101373567	101373567	+	stop_gained	Nonsense_Mutation	SNP	G	G	A			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41	32			ENST00000312938.4:c.2290C>T	p.Arg764Ter	p.R764*	ENST00000312938	NM_014415.3	764	Cga/Tga	0	0.363	TGATAGCCTCGAACCTCAGGC
ZBTB20	26137	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	114058129	114058129	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	154	79			ENST00000474710.1:c.1949A>G	p.Asn650Ser	p.N650S	ENST00000474710	NM_001164342.1	650	aAc/aGc	0	0.527	CATGTGCACGTTGAGGGAGCT
IGSF10	285313	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	151162901	151162901	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	65	51			ENST00000282466.3:c.4868A>G	p.Lys1623Arg	p.K1623R	ENST00000282466	NM_178822.4	1623	aAg/aGg	0	0.438	AACTGGTTTCTTATCAAAGTC
PIK3CA	5290	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273		TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23	17			ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	0	0.333	TCCTCTCTCTGAAATCACTGA
PCDHGC3	5098	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	140857769	140857769	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	279	208			ENST00000308177.3:c.2086C>A	p.Leu696Ile	p.L696I	ENST00000308177	NM_002588.2	696	Ctt/Att	0	0.488	TTATCTACTTCTTTCTCTAAT
EZR	7430	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	159188410	159188410	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	104	51			ENST00000367075.3:c.1479C>T	p.Gly493=	p.G493=	ENST00000367075	NM_001111077.1	493	ggC/ggT	0	0.642	TGGGCTCTGCGCCCTCATCCT
AGR3	155465	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	16918142	16918142	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	32	19			ENST00000310398.2:c.101T>C	p.Leu34Pro	p.L34P	ENST00000310398	NM_176813.3	34	cTc/cCc	0	0.383	ACCTCTTGAGAGTGTCTGAGG
SKAP2	8935	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	26729921	26729921	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	49	25			ENST00000345317.2:c.857G>A	p.Ser286Asn	p.S286N	ENST00000345317	NM_003930.3	286	aGt/aAt	0	0.378	GTGATGGACACTATCCTGACT
MCPH1	79648	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	6301937	6301937	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	38	22			ENST00000344683.5:c.694C>T	p.His232Tyr	p.H232Y	ENST00000344683	NM_024596.3	232	Cac/Tac	0	0.338	TGGTGGCTTACACTCATCTTT
WNK2	65268	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	96018613	96018613	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14	7			ENST00000297954.4:c.2067C>T	p.Pro689=	p.P689=	ENST00000297954	NM_001282394.1	689	ccC/ccT	0	0.751	TCCCGGCCCCCGCCTGCCCTC
AGPAT2	10555	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	139571516	139571516	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	134	75			ENST00000371696.2:c.389G>A	p.Gly130Asp	p.G130D	ENST00000371696	NM_006412.3	130	gGc/gAc	0	0.637	CATGATGAGGCCCACGGGCCC
ASMTL	8623	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	1551213	1551213	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	20	33			ENST00000381317.3:c.458C>T	p.Ser153Leu	p.S153L	ENST00000381317	NM_004192.3	153	tCg/tTg	0	0.637	GGACAGCTCCGAGAACTTCAC
NHS	4810	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	17744930	17744930	+	stop_gained	Nonsense_Mutation	SNP	G	G	T			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	80	68			ENST00000380060.3:c.2641G>T	p.Glu881Ter	p.E881*	ENST00000380060	NM_198270.2	881	Gaa/Taa	0	0.468	TTCTCGAATGGAAAACGCCAA
GK	2710	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	30739086	30739086	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29	23			ENST00000378943.3:c.1457G>A	p.Arg486Gln	p.R486Q	ENST00000378943	NM_001128127.2	486	cGg/cAg	0	0.502	ACGATGGAGCGGTTTGAACCT
TRO	7216	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	54957391	54957391	+	missense_variant	Missense_Mutation	SNP	A	A	T			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30	25			ENST00000173898.7:c.4234A>T	p.Thr1412Ser	p.T1412S	ENST00000173898	NM_001039705.2	1412	Acc/Tcc	0	0.587	TGGACCGAGCACCAGTGCTGG
PBDC1	51260	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	75397598	75397598	+	missense_variant	Missense_Mutation	SNP	A	A	T			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	16	11			ENST00000373358.3:c.557A>T	p.Asn186Ile	p.N186I	ENST00000373358	NM_016500.3	186	aAc/aTc	0	0.413	gaagaagagaacaccaagaat
USP26	83844	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	132159579	132159579	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	43	30			ENST00000511190.1:c.2670A>G	p.Glu890=	p.E890=	ENST00000511190	NM_031907.1	890	gaA/gaG	0	0.458	TCAACATCTCTTCAAAGATCT
GPR112	139378	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	135405392	135405392	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98	85			ENST00000394143.1:c.526C>T	p.Arg176Cys	p.R176C	ENST00000394143	NM_153834.3	176	Cgt/Tgt	0	0.448	AAGCATGATGCGTAGCTTTCC
AFF2	2334	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	148068962	148068962	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91	67			ENST00000370460.2:c.3689A>G	p.Asn1230Ser	p.N1230S	ENST00000370460	NM_002025.3	1230	aAt/aGt	0	0.532	AACTGTAACAATGGCCCAGTC
COL8A1	1295	broad.mit.edu;ucsc.edu	GRCh37	3	99513494	99513494	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	129	68			ENST00000261037.3:c.749C>T	p.Ala250Val	p.A250V	ENST00000261037	NM_001850.4	250	gCg/gTg	0	0.642	ATGCCAGGTGCGCCAGGTGTA
HECW1	23072	broad.mit.edu;ucsc.edu	GRCh37	7	43483866	43483866	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47	21			ENST00000395891.2:c.1095G>A	p.Gln365=	p.Q365=	ENST00000395891	NM_015052.3	365	caG/caA	0	0.532	CCCAAATTCAGGACAGCCCCA
TDGF1P3	6998	broad.mit.edu;ucsc.edu	GRCh37	X	109764561	109764561	+	non_coding_transcript_exon_variant	RNA	SNP	G	G	A			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	55	47			ENST00000602699.1:n.1022G>A		*341*	ENST00000602699				0	0.572	AGCGTGTGCTGCCCATGGGAA
ZCCHC10	54819	broad.mit.edu;hgsc.bcm.edu	GRCh37	5	132334445	132334446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	22	12			ENST00000324170.3:c.342dupA	p.Glu115ArgfsTer4	p.E115Rfs*4	ENST00000324170	NM_017665.1	114	-/A	0	0.48	TCACTGTCCTCTGAGGAGGAAG
ZNF292	23036	broad.mit.edu;hgsc.bcm.edu	GRCh37	6	87964502	87964503	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39	19			ENST00000369577.3:c.1158dupA	p.Arg387ThrfsTer7	p.R387Tfs*7	ENST00000369577	NM_015021.1	385	-/A	0	0.376	ATCTGGAAGTTAAACGTGCTTG
BCOR	54880	broad.mit.edu;hgsc.bcm.edu	GRCh37	X	39930292	39930292	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-			TCGA-DB-A64W-01	TCGA-DB-A64W-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58	40			ENST00000378444.4:c.3172delC	p.Gln1058ArgfsTer55	p.Q1058Rfs*55	ENST00000378444	NM_001123385.1	1058	Cag/ag	0	0.493	TTTTTGTCCTGATTTCCTTTC
PPFIA1	8500	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	70208264	70208264	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-E1-5311-01	TCGA-E1-5311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	109	71			ENST00000253925.7:c.2646G>A	p.Thr882=	p.T882=	ENST00000253925	NM_003626.3	882	acG/acA	0	0.448	ACGGGCCAACGGTTGTGGTCT
SSH2	85464	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	27994187	27994187	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-E1-5311-01	TCGA-E1-5311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	114	53			ENST00000269033.3:c.783C>T	p.Ile261=	p.I261=	ENST00000269033	NM_033389.2	261	atC/atT	0	0.383	TCTGCATCATGATCTCCCTTA
CIC	23152	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	42791718	42791718	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-E1-5311-01	TCGA-E1-5311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28	54			ENST00000575354.2:c.604C>T	p.Arg202Trp	p.R202W	ENST00000575354	NM_015125.3	202	Cgg/Tgg	0	0.622	CCACATCCGGCGGCCCATGAA
ECM1	1893	hgsc.bcm.edu;broad.mit.edu	GRCh37	1	150482440	150482440	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-E1-5311-01	TCGA-E1-5311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	207	10			ENST00000369049.4:c.347A>G	p.Glu116Gly	p.E116G	ENST00000369049	NM_001202858.1	116	gAa/gGa	0	0.597	CTCCAACAGGAAAAGCTGCTA
PLCB1	23236	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	20	8862304	8862304	+	missense_variant	Missense_Mutation	SNP	A	A	C			TCGA-E1-5311-01	TCGA-E1-5311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257	167			ENST00000338037.6:c.3459A>C	p.Lys1153Asn	p.K1153N	ENST00000338037	NM_015192.3	1153	aaA/aaC	0	0.468	ACCAAGACAAATTCAAAAGAC
TCFL5	10732	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	20	61488943	61488943	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-E1-5311-01	TCGA-E1-5311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	142	88			ENST00000335351.3:c.1042C>T	p.Arg348Cys	p.R348C	ENST00000335351	NM_006602.2	348	Cgt/Tgt	0	0.463	TCCAACTGACGCATTCTACTC
HEATR5B	54497	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	37265041	37265041	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-E1-5311-01	TCGA-E1-5311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90	56			ENST00000233099.5:c.3173C>T	p.Ala1058Val	p.A1058V	ENST00000233099	NM_019024.1	1058	gCa/gTa	0	0.383	ATGTCGTGGTGCAAACATGTG
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-E1-5311-01	TCGA-E1-5311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	94	73			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
FRAS1	80144	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	79420950	79420950	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-E1-5311-01	TCGA-E1-5311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	150	108			ENST00000264895.6:c.9191A>G	p.Asn3064Ser	p.N3064S	ENST00000264895	NM_025074.6	3064	aAc/aGc	0	0.532	GCGATTCTGAACATCAAGGTG
IL15	3600	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	142651106	142651106	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-E1-5311-01	TCGA-E1-5311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	179	63			ENST00000296545.7:c.347T>C	p.Ile116Thr	p.I116T	ENST00000296545		116	aTc/aCc	0	0.388	AATCTGATCATCCTAGCAAAC
PCDHGA3	56112	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	140724038	140724038	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-E1-5311-01	TCGA-E1-5311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68	78			ENST00000253812.6:c.438G>A	p.Thr146=	p.T146=	ENST00000253812	NM_018916.3	146	acG/acA	0	0.353	GTGAACTAACGGTTCCTGGAA
KIAA1324L	222223	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	86526826	86526826	+	missense_variant	Missense_Mutation	SNP	A	A	C			TCGA-E1-5311-01	TCGA-E1-5311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	140	72			ENST00000450689.2:c.2681T>G	p.Phe894Cys	p.F894C	ENST00000450689	NM_001142749.2	894	tTt/tGt	0	0.468	CCTTACCTGAAATCCTCTCTT
KCNU1	157855	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	36766859	36766859	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-E1-5311-01	TCGA-E1-5311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	395	255			ENST00000399881.3:c.2137C>T	p.Arg713Trp	p.R713W	ENST00000399881	NM_001031836.2	713	Cgg/Tgg	0	0.468	GTATAAGTTTCGGAACCATAT
NOTCH1	4851	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	139412204	139412204	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G			TCGA-E1-5311-01	TCGA-E1-5311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	80	43			ENST00000277541.6:c.1441G>C	p.Gly481Arg	p.G481R	ENST00000277541	NM_017617.3	481	Ggc/Cgc	0	0.667	GCCGACGCACCGGGCATGCAG
SMC4	10051	broad.mit.edu;ucsc.edu	GRCh37	3	160141575	160141575	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-E1-5311-01	TCGA-E1-5311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	144	34			ENST00000357388.3:c.2272G>C	p.Val758Leu	p.V758L	ENST00000357388	NM_001002800.1	758	Gta/Cta	0	0.383	TGGAAGCAAAGTAATGAAAGG
ANKRD11	29123	broad.mit.edu;ucsc.edu	GRCh37	16	89350191	89350191	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-E1-5311-01	TCGA-E1-5311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	211	108			ENST00000301030.4:c.2759G>A	p.Arg920Lys	p.R920K	ENST00000301030	NM_001256183.1	920	aGg/aAg	0	0.547	CTGCTCTTTCCTCTTCTCAGA
DNM1P46	196968	broad.mit.edu;ucsc.edu	GRCh37	15	100332827	100332827	+	non_coding_transcript_exon_variant	RNA	SNP	G	G	A			TCGA-E1-5311-01	TCGA-E1-5311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	22	26			ENST00000341853.1:n.1365C>T		*455*	ENST00000341853				0	0.612	TGACTACAACGAGGGACACAG
ITIH2	3698	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	7780699	7780699	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	44	12			ENST00000358415.4:c.2073G>A	p.Thr691=	p.T691=	ENST00000358415	NM_002216.2	691	acG/acA	0	0.562	TAGAGTCCACGCCACCCCCAC
RAG1	5896	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	36596675	36596675	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	34	11			ENST00000299440.5:c.1821C>T	p.Asp607=	p.D607=	ENST00000299440	NM_000448.2	607	gaC/gaT	0	0.468	GAATGGGAGACGTGAGTGAGA
SORL1	6653	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	121421301	121421301	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	65	7			ENST00000260197.7:c.2188A>G	p.Lys730Glu	p.K730E	ENST00000260197	NM_003105.5	730	Aag/Gag	0	0.557	CAGCTACCGGAAGATTTCTGG
KCNMB4	27345	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	70824288	70824288	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	152	19			ENST00000258111.4:c.488G>A	p.Arg163His	p.R163H	ENST00000258111	NM_014505.5	163	cGc/cAc	0	0.488	CTTCTGCATCGCACTCATGAT
HECTD4	283450	hgsc.bcm.edu;broad.mit.edu	GRCh37	12	112617095	112617095	+	synonymous_variant	Silent	SNP	G	G	C			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14	6			ENST00000550722.1:c.10656C>G	p.Val3552=	p.V3552=	ENST00000550722	NM_001109662.3	3552	gtC/gtG	0	0.542	AAATGTCAGAGACTCTGATGG
SOHLH2	54937	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	13	36776075	36776075	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71	23			ENST00000511166.1:c.435T>C	p.Val145=	p.V145=	ENST00000511166	NM_001198910.1	145	gtT/gtC	0	0.423	CCTTCAAGAGAACCATGTTGA
FNDC3A	22862	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	13	49710555	49710555	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26	27			ENST00000492622.2:c.578G>A	p.Arg193His	p.R193H	ENST00000492622	NM_001079673.1	193	cGc/cAc	0	0.388	TTGAAGGATCGCCAAGGAACA
NGDN	25983	hgsc.bcm.edu;broad.mit.edu	GRCh37	14	23940135	23940135	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	101	6			ENST00000408901.3:c.93A>G	p.Gln31=	p.Q31=	ENST00000408901	NM_015514.1	31	caA/caG	0	0.368	TAACTGCACAAGTGAAATCAC
CTAGE5	4253	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	14	39784908	39784908	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88	26			ENST00000396158.2:c.1393G>A	p.Ala465Thr	p.A465T	ENST00000396158	NM_001247989.1	465	Gca/Aca	0	0.254	TGAGAAAAAAGCACATGATAA
EIF2AK4	440275	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	40241413	40241413	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79	47			ENST00000263791.5:c.457C>T	p.Arg153Trp	p.R153W	ENST00000263791	NM_001013703.2	153	Cgg/Tgg	0	0.537	GCTGGAAAGGCGGGCTCAGGA
BUB1B	701	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	40509802	40509802	+	synonymous_variant	Silent	SNP	C	C	T	rs139066741	by1000genomes	TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	305	95			ENST00000287598.6:c.2784C>T	p.Ser928=	p.S928=	ENST00000287598	NM_001211.5	928	agC/agT	0	0.443	TTACCCTCAGCGGCTTTCGGA
TP53	7157	hgsc.bcm.edu;broad.mit.edu	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343		TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3	23			ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	0	0.542	GCACAAACACGCACCTCAAAG
CTC1	80169	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	8132163	8132163	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	20	4			ENST00000315684.8:c.3269A>G	p.Asn1090Ser	p.N1090S	ENST00000315684	NM_025099.5	1090	aAt/aGt	0	0.567	CACATGGTGATTCCTACAGGT
PSMD3	5709	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	38151212	38151212	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45	19			ENST00000264639.4:c.987C>G	p.His329Gln	p.H329Q	ENST00000264639	NM_002809.3	329	caC/caG	0	0.572	TCCAGGTGCACAAGCTTCTCA
CCR7	1236	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	38711759	38711759	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	20	19			ENST00000246657.2:c.372C>T	p.Phe124=	p.F124=	ENST00000246657	NM_001838.3	124	ttC/ttT	0	0.552	AGTGGACACCGAAGACCCAGG
HDAC5	10014	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	42169818	42169818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138137922		TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	13	10			ENST00000225983.6:c.853C>T	p.Arg285Cys	p.R285C	ENST00000225983		285	Cgc/Tgc	0	0.537	CCATCCTTGCGACGCAGGAGG
KLHL14	57565	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	18	30349844	30349844	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30	10			ENST00000359358.4:c.711G>A	p.Ala237=	p.A237=	ENST00000359358	NM_020805.1	237	gcG/gcA	0	0.657	TCTGGAAGAGCGCCAGCTCCG
FCGBP	8857	hgsc.bcm.edu;broad.mit.edu	GRCh37	19	40408740	40408740	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	32	16			ENST00000221347.6:c.4099G>A	p.Ala1367Thr	p.A1367T	ENST00000221347	NM_003890.2	1367	Gcc/Acc	0	0.587	AGGTCGTAGGCCACACGCAGG
MST1L	11223	hgsc.bcm.edu;broad.mit.edu	GRCh37	1	17084292	17084292	+	non_coding_transcript_exon_variant	RNA	SNP	A	A	G			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	181	27			ENST00000389184.2:n.1710T>C		*570*	ENST00000389184				0	0.587	TGGTCCCTGGAGGCACCACAT
MST1L	11223	hgsc.bcm.edu;broad.mit.edu	GRCh37	1	17084293	17084293	+	non_coding_transcript_exon_variant	RNA	SNP	G	G	T			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	179	26			ENST00000389184.2:n.1709C>A		*570*	ENST00000389184				0	0.587	GGTCCCTGGAGGCACCACATA
SCMH1	22955	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	41579187	41579187	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24	14			ENST00000402904.2:c.483G>A	p.Ser161=	p.S161=	ENST00000402904	NM_001031694.2	161	tcG/tcA	0	0.443	TGTGGGAAGGCGATGGTGGCT
CFHR5	81494	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	196973949	196973949	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58	25			ENST00000256785.4:c.1489T>C	p.Trp497Arg	p.W497R	ENST00000256785		497	Tgg/Cgg	0	0.378	AAATAAACAGTGGTCAGAACC
HHIPL2	79802	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	222717481	222717481	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	159	40			ENST00000343410.6:c.372G>A	p.Thr124=	p.T124=	ENST00000343410	NM_024746.3	124	acG/acA	0	0.597	TCCGGAGAGGCGTCTGGGTGT
PRND	23627	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	20	4705632	4705632	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	38	8			ENST00000305817.2:c.435C>T	p.Cys145=	p.C145=	ENST00000305817	NM_012409.2	145	tgC/tgT	0	0.602	TCAAGCATTGCGAGTTTTGGT
PLCG1	5335	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	20	39795459	39795459	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	55	33			ENST00000373272.2:c.2261A>G	p.Tyr754Cys	p.Y754C	ENST00000373272	NM_002660.2	754	tAt/tGt	0	0.562	AAGCTGCGCTATCCCATCAAC
MAP3K19	80122	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	135744754	135744754	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98	16			ENST00000375845.3:c.1688C>T	p.Thr563Ile	p.T563I	ENST00000375845	NM_025052.3	563	aCc/aTc	0	0.423	TTTATGCATGGTAGGCTTAAT
IFIH1	64135	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	163134056	163134056	+	missense_variant	Missense_Mutation	SNP	A	A	C			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	19	17			ENST00000263642.2:c.1913T>G	p.Phe638Cys	p.F638C	ENST00000263642	NM_022168.3	638	tTt/tGt	0	0.353	TATGACTGCAAACTTCTTATC
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52	24			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
FLNB	2317	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	58094210	58094210	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21	12			ENST00000490882.1:c.1967A>G	p.Glu656Gly	p.E656G	ENST00000490882	NM_001164317.1	656	gAg/gGg	0	0.448	CCAGGTTTGGAGAAATCTGGA
LEKR1	389170	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	156763496	156763496	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58	31			ENST00000356539.4:c.2036A>G	p.Gln679Arg	p.Q679R	ENST00000356539	NM_001004316.2	679	cAg/cGg	0	0.547	GAGACTAGACAGAGACTGGCT
IGF2BP2	10644	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	185393095	185393095	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	134	17			ENST00000382199.2:c.1060C>T	p.Leu354=	p.L354=	ENST00000382199	NM_006548.4	354	Ctg/Ttg	0	0.463	TTAACAGCCAGCATATCATTT
ANK2	287	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	114280346	114280346	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	77	17			ENST00000357077.4:c.10572C>T	p.Thr3524=	p.T3524=	ENST00000357077	NM_001148.4	3524	acC/acT	0	0.473	CTGTTGAGACCGAGCACTCAG
SEC24D	9871	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	119649799	119649799	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	51	9			ENST00000280551.6:c.2875C>T	p.Leu959=	p.L959=	ENST00000280551		959	Ctg/Ttg	0	0.303	ACTTCAGGCAGCAATGTCTTA
GFM2	84340	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	74034187	74034187	+	missense_variant	Missense_Mutation	SNP	A	A	C			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	83	88			ENST00000296805.3:c.1276T>G	p.Ser426Ala	p.S426A	ENST00000296805	NM_032380.4	426	Tca/Gca	0	0.333	GCAGTCAATGAAGGGATTTCT
PCDHAC1	56135	hgsc.bcm.edu;broad.mit.edu	GRCh37	5	140308171	140308171	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	108	7			ENST00000253807.2:c.1694T>C	p.Val565Ala	p.V565A	ENST00000253807	NM_018898.3	565	gTc/gCc	0	0.473	AATGGTTCTGTCCCAGTGGAA
STK10	6793	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	171520604	171520604	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	56	10			ENST00000176763.5:c.1366G>A	p.Ala456Thr	p.A456T	ENST00000176763	NM_005990.3	456	Gcc/Acc	0	0.647	GTCTCCAGGGCGCTGCTGTTG
NPC1L1	29881	hgsc.bcm.edu;ucsc.edu	GRCh37	7	44579068	44579068	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs79803700	byFrequency	TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98	19			ENST00000289547.4:c.928G>A	p.Ala310Thr	p.A310T	ENST00000289547	NM_013389.2	310	Gcc/Acc	0	0.602	TTGTCCCTGGCGGGGGCCACA
LMTK2	22853	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	97823142	97823142	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39	29			ENST00000297293.5:c.3365G>A	p.Gly1122Glu	p.G1122E	ENST00000297293	NM_014916.3	1122	gGa/gAa	0	0.607	GAGGTCCCGGGAACCTCCCCA
COG5	10466	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	107204267	107204267	+	synonymous_variant	Silent	SNP	G	G	C			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24	11			ENST00000297135.3:c.168C>G	p.Val56=	p.V56=	ENST00000297135	NM_006348.3	56	gtC/gtG	0	0.667	GAAGTTCCCGGACTGTAGCTG
PLXNA4	91584	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	131848964	131848964	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	32	8			ENST00000359827.3:c.4437C>T	p.Gly1479=	p.G1479=	ENST00000359827		1479	ggC/ggT	0	0.592	AGCGGGCCTCGCCCGTGATGG
SHH	6469	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	155599004	155599004	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88	25			ENST00000297261.2:c.548G>A	p.Cys183Tyr	p.C183Y	ENST00000297261	NM_000193.2	183	tGc/tAc	0	0.622	TTTCACCGAGCAGTGGATATG
EPPK1	83481	hgsc.bcm.edu;broad.mit.edu	GRCh37	8	144942235	144942235	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58	35			ENST00000525985.1:c.5187C>T	p.Phe1729=	p.F1729=	ENST00000525985	NM_031308.2	1729	ttC/ttT	0	0.622	TGTTGGGGTCGAAGAAGCCCT
SVEP1	79987	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	113139596	113139596	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45	20			ENST00000401783.2:c.10459G>T	p.Ala3487Ser	p.A3487S	ENST00000401783	NM_153366.3	3487	Gct/Tct	0	0.507	CAGGAACAAGCATTTGGGCGT
MAGEB10	139422	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	27840125	27840125	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	44	8			ENST00000356790.2:c.702C>T	p.Asp234=	p.D234=	ENST00000356790	NM_182506.3	234	gaC/gaT	0	0.468	GGTTATATGACGGAATTGAGC
ARHGEF6	9459	hgsc.bcm.edu;broad.mit.edu	GRCh37	X	135825810	135825810	+	stop_gained	Nonsense_Mutation	SNP	C	C	A			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	222	13			ENST00000250617.6:c.595G>T	p.Glu199Ter	p.E199*	ENST00000250617	NM_004840.2	199	Gaa/Taa	0	0.408	AATGTGCCTTCCCACCAGCCT
MAGEC3	139081	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	140969496	140969496	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	215	32			ENST00000298296.1:c.823C>A	p.Leu275Ile	p.L275I	ENST00000298296	NM_138702.1	275	Ctc/Atc	0	0.502	CCAGAACCGCCTCCTGATTCT
TMEM9	252839	broad.mit.edu;ucsc.edu	GRCh37	1	201112999	201112999	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42	4			ENST00000367330.1:c.348C>G	p.Ile116Met	p.I116M	ENST00000367330	NM_001288565.1	116	atC/atG	0	0.572	CCGGCTTTCGGATCAGAGGGT
FOSB	2354	broad.mit.edu;ucsc.edu	GRCh37	19	45974181	45974181	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28	15			ENST00000353609.3:c.421C>T	p.Arg141Trp	p.R141W	ENST00000353609	NM_006732.2	141	Cgg/Tgg	0	0.632	AGCCCGAGCCCGGCCTAGGAG
MDM4	4194	broad.mit.edu;ucsc.edu	GRCh37	1	204518349	204518349	+	missense_variant	Missense_Mutation	SNP	A	A	C			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	121	15			ENST00000367182.3:c.1012A>C	p.Thr338Pro	p.T338P	ENST00000367182	NM_001278516.1	338	Acc/Ccc	0	0.428	TTCAAAGTTAACCCATTCTCT
KRT73	319101	broad.mit.edu;ucsc.edu	GRCh37	12	53008406	53008406	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47	5			ENST00000305748.3:c.776C>T	p.Ala259Val	p.A259V	ENST00000305748	NM_175068.2	259	gCc/gTc	0	0.542	TCCATCCAGGGCATCCACCTT
ATRX	546	broad.mit.edu;ucsc.edu	GRCh37	X	76909629	76909629	+	stop_gained	Nonsense_Mutation	SNP	G	G	A			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	102	41			ENST00000373344.5:c.4276C>T	p.Arg1426Ter	p.R1426*	ENST00000373344	NM_000489.3	1426	Cga/Tga	0	0.328	TTAATACGTCGCCTTTTCTTT
ASB9	140462	broad.mit.edu;ucsc.edu	GRCh37	X	15272893	15272893	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	205	25			ENST00000380488.4:c.248C>T	p.Ser83Phe	p.S83F	ENST00000380488	NM_001031739.2	83	tCt/tTt	0	0.443	CTTCACACAAGAGAGATGACC
PTPRF	5792	broad.mit.edu;ucsc.edu	GRCh37	1	44079328	44079328	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45	19			ENST00000359947.4:c.4013C>T	p.Ala1338Val	p.A1338V	ENST00000359947	NM_002840.3	1338	gCg/gTg	0	0.597	ACCGACCTGGCGGACAACATC
ARID2	196528	broad.mit.edu;hgsc.bcm.edu	GRCh37	12	46245951	46245960	+	frameshift_variant	Frame_Shift_Del	DEL	ATCAAAAGTG	ATCAAAAGTG	-			TCGA-DU-5855-01	TCGA-DU-5855-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41	19			ENST00000334344.6:c.4047_4056delCAAAAGTGAT	p.Lys1350Ter	p.K1350*	ENST00000334344	NM_152641.2	1349	ATCAAAAGTGat/at	0	0.357	CATGCAAGATATCAAAAGTGATTTGAGAAA
TMX2	51075	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	57480129	57480129	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-A616-01	TCGA-HT-A616-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40	7			ENST00000278422.4:c.39G>A	p.Ser13=	p.S13=	ENST00000278422	NM_015959.3	13	tcG/tcA	0	0.627	TCGTGTATTCGGTGCCGCGAC
THBS1	7057	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	39884880	39884880	+	stop_gained	Nonsense_Mutation	SNP	C	C	T			TCGA-HT-A616-01	TCGA-HT-A616-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36	18			ENST00000260356.5:c.2644C>T	p.Gln882Ter	p.Q882*	ENST00000260356	NM_003246.2	882	Cag/Tag	0	0.502	CAATGCCAACCAGGCTGACCA
SPINT1	6692	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	41146276	41146276	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138167951		TCGA-HT-A616-01	TCGA-HT-A616-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	126	52			ENST00000344051.4:c.980G>A	p.Arg327His	p.R327H	ENST00000344051		327	cGc/cAc	0	0.592	ATGGAAAGGCGCCATCCAGGT
ANKRD13B	124930	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	27939276	27939276	+	missense_variant	Missense_Mutation	SNP	T	T	G			TCGA-HT-A616-01	TCGA-HT-A616-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	86	32			ENST00000394859.3:c.1243T>G	p.Phe415Val	p.F415V	ENST00000394859	NM_152345.4	415	Ttc/Gtc	0	0.622	GCCTCCTGGCTTCCCAGTTAA
ABCA9	10350	hgsc.bcm.edu;broad.mit.edu	GRCh37	17	66982397	66982397	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-A616-01	TCGA-HT-A616-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	119	8			ENST00000340001.4:c.4116G>A	p.Ala1372=	p.A1372=	ENST00000340001	NM_080283.3	1372	gcG/gcA	0	0.547	TGGGCCACAGCGCATTCTCCT
DSG2	1829	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	18	29126141	29126141	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-HT-A616-01	TCGA-HT-A616-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78	66			ENST00000261590.8:c.2792G>C	p.Arg931Thr	p.R931T	ENST00000261590	NM_001943.3	931	aGa/aCa	0	0.473	ATGGCTTCTAGAAATGTGATA
RTTN	25914	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	18	67695981	67695981	+	synonymous_variant	Silent	SNP	A	A	C			TCGA-HT-A616-01	TCGA-HT-A616-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	20	5			ENST00000255674.6:c.5802T>G	p.Leu1934=	p.L1934=	ENST00000255674	NM_173630.3	1934	ctT/ctG	0	0.308	CATTTTGATAAAGACAGTTTC
PRODH2	58510	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	36293163	36293163	+	synonymous_variant	Silent	SNP	G	G	T			TCGA-HT-A616-01	TCGA-HT-A616-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	148	13			ENST00000301175.3:c.1356C>A	p.Gly452=	p.G452=	ENST00000301175	NM_021232.1	452	ggC/ggA	0	0.542	CCAGAGGAATGCCCAGCTCCC
KCNA7	3743	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	49573516	49573516	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-A616-01	TCGA-HT-A616-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	43	26			ENST00000221444.1:c.1175T>C	p.Val392Ala	p.V392A	ENST00000221444	NM_031886.2	392	gTc/gCc	0	0.567	GGAGACAATGACGGGCACTGG
PRR12	57479	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	50123629	50123629	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-A616-01	TCGA-HT-A616-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	16	7			ENST00000418929.2:c.5518C>T	p.Leu1840=	p.L1840=	ENST00000418929	NM_020719.1	1840	Ctg/Ttg	0	0.567	ACCTGGGCGTCTGCTCAAAAC
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	179453926	179453926	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-HT-A616-01	TCGA-HT-A616-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67	54			ENST00000589042.1:c.62526T>C	p.Tyr20842=	p.Y20842=	ENST00000589042	NM_001267550.1	20842	taT/taC	0	0.413	CCGTAACTACATATTTACCCC
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	179579894	179579894	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-A616-01	TCGA-HT-A616-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	105	62			ENST00000589042.1:c.26019C>T	p.His8673=	p.H8673=	ENST00000589042	NM_001267550.1	8673	caC/caT	0	0.443	ACCAAGAAACGTGAAATGGGG
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HT-A616-01	TCGA-HT-A616-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	51	16			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
CCDC54	84692	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	107096617	107096617	+	synonymous_variant	Silent	SNP	C	C	T	rs144553244		TCGA-HT-A616-01	TCGA-HT-A616-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	85	29			ENST00000261058.1:c.183C>T	p.Asp61=	p.D61=	ENST00000261058	NM_032600.2	61	gaC/gaT	0	0.363	ATAGTTATGACGGAAAAATGA
CAPN11	11131	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	44143857	44143857	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-A616-01	TCGA-HT-A616-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28	8			ENST00000398776.1:c.884G>A	p.Gly295Glu	p.G295E	ENST00000398776	NM_007058.3	295	gGg/gAg	0	0.557	CTGGTGAGAGGGCACGCTTAC
MAGEB4	4115	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	30260295	30260295	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-A616-01	TCGA-HT-A616-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52	16			ENST00000378982.2:c.43C>T	p.Arg15Cys	p.R15C	ENST00000378982	NM_002367.3	15	Cgc/Tgc	0	0.567	CCGTGAGAAACGCCAGCGGAC
ATRX	546	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	76939697	76939697	+	stop_gained	Nonsense_Mutation	SNP	C	C	A			TCGA-HT-A616-01	TCGA-HT-A616-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71	39			ENST00000373344.5:c.1051G>T	p.Glu351Ter	p.E351*	ENST00000373344	NM_000489.3	351	Gag/Tag	0	0.353	TTAATCATCTCTTTGGGCACA
RGAG1	57529	hgsc.bcm.edu;broad.mit.edu	GRCh37	X	109694050	109694050	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-HT-A616-01	TCGA-HT-A616-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	316	26			ENST00000465301.2:c.205C>G	p.Pro69Ala	p.P69A	ENST00000465301	NM_020769.2	69	Cca/Gca	0	0.517	GATGACATCTCCAGTCTTTGA
MCF2	4168	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	138711938	138711938	+	missense_variant	Missense_Mutation	SNP	T	T	A			TCGA-HT-A616-01	TCGA-HT-A616-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	147	82			ENST00000519895.1:c.534A>T	p.Glu178Asp	p.E178D	ENST00000519895	NM_001171876.1	178	gaA/gaT	0	0.398	TCTCAGCCAGTTCAGTTCCAA
CD99L2	83692	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	149938823	149938823	+	synonymous_variant	Silent	SNP	G	G	A	rs147156476	byFrequency	TCGA-HT-A616-01	TCGA-HT-A616-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39	20			ENST00000370377.3:c.675C>T	p.Tyr225=	p.Y225=	ENST00000370377	NM_031462.3	225	taC/taT	0	0.537	CTCCCTTCACGTAGTCTGCGT
HMGB3	3149	hgsc.bcm.edu;broad.mit.edu	GRCh37	X	150156360	150156360	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-A616-01	TCGA-HT-A616-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62	5			ENST00000325307.7:c.576G>A	p.Glu192=	p.E192=	ENST00000325307	NM_005342.2	192	gaG/gaA	0	0.443	aggaagaagaggaggaggagg
KIAA1324	57535	broad.mit.edu;ucsc.edu	GRCh37	1	109741239	109741239	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-HT-A616-01	TCGA-HT-A616-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17	3			ENST00000369939.3:c.2444C>G	p.Thr815Ser	p.T815S	ENST00000369939	NM_020775.4	815	aCc/aGc	0	0.532	AGATCAACCACCATCCGCGTC
CCAR1	55749	broad.mit.edu;hgsc.bcm.edu	GRCh37	10	70513778	70513779	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A			TCGA-HT-A616-01	TCGA-HT-A616-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69	32			ENST00000265872.6:c.1295dupA	p.Asn432LysfsTer6	p.N432Kfs*6	ENST00000265872	NM_018237.2	430	gaa/gAaa	0	0.381	AGAGTCCTTAGAAAAAAATATG
FPR3	2359	hgsc.bcm.edu;broad.mit.edu	GRCh37	19	52327322	52327322	+	synonymous_variant	Silent	SNP	C	C	A			TCGA-P5-A5EY-01	TCGA-P5-A5EY-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	87	7			ENST00000339223.4:c.321C>A	p.Ile107=	p.I107=	ENST00000339223	NM_002030.3	107	atC/atA	0	0.478	TGATAGACATCAACCTGTTTG
ROM1	6094	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	62380964	62380964	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-8114-01	TCGA-HT-8114-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30	5			ENST00000278833.3:c.211G>A	p.Ala71Thr	p.A71T	ENST00000278833	NM_000327.3	71	Gcg/Acg	0	0.667	GGCAGCGGGCGCGGTGGCTCT
SRPR	6734	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	126134414	126134414	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-8114-01	TCGA-HT-8114-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61	8			ENST00000332118.6:c.1546G>A	p.Val516Met	p.V516M	ENST00000332118	NM_003139.3	516	Gtg/Atg	0	0.507	ACCAGCACCACGTCAAAGCCT
GAS6	2621	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	13	114531664	114531664	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-8114-01	TCGA-HT-8114-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78	13			ENST00000327773.6:c.1164G>A	p.Ala388=	p.A388=	ENST00000327773	NM_000820.2	388	gcG/gcA	0	0.537	CCAGATTCCGCGCCAGCTCCT
ZC3H14	79882	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	14	89044401	89044401	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-8114-01	TCGA-HT-8114-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75	28			ENST00000251038.5:c.1196T>C	p.Val399Ala	p.V399A	ENST00000251038	NM_024824.4	399	gTc/gCc	0	0.388	GCAGAAGTGGTCCAGGGACAA
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C			TCGA-HT-8114-01	TCGA-HT-8114-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	16	29			ENST00000269305.4:c.560-2A>G		p.X187_splice	ENST00000269305	NM_001126112.2			0	0.552	GGGCCAGACCTAAGAGCAATC
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-8114-01	TCGA-HT-8114-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61	10			ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	0	0.642	GCAGCGCTCATGGTGGGGGCA
ZNF235	9310	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	44793178	44793178	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-8114-01	TCGA-HT-8114-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	126	10			ENST00000291182.4:c.410A>G	p.His137Arg	p.H137R	ENST00000291182	NM_004234.4	137	cAt/cGt	0	0.438	GGGGGAATCATGGTGCTTGGG
ITSN1	6453	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	21	35183494	35183494	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-8114-01	TCGA-HT-8114-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	113	10			ENST00000381318.3:c.2535G>A	p.Thr845=	p.T845=	ENST00000381318	NM_003024.2	845	acG/acA	0	0.547	AGCCCTCCACGACCCCTAATA
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HT-8114-01	TCGA-HT-8114-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	50	46			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
PCDH12	51294	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	141325159	141325159	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-HT-8114-01	TCGA-HT-8114-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	46	5			ENST00000231484.3:c.3342C>G	p.Ser1114Arg	p.S1114R	ENST00000231484	NM_016580.3	1114	agC/agG	0	0.662	CCAGCAGTGAGCTCATCTCCG
FAT2	2196	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	150932869	150932869	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-8114-01	TCGA-HT-8114-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57	23			ENST00000261800.5:c.4025C>T	p.Pro1342Leu	p.P1342L	ENST00000261800	NM_001447.2	1342	cCg/cTg	0	0.582	GATGGAGGACGGCCGGGGCCA
ATAD2	29028	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	124351613	124351613	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-8114-01	TCGA-HT-8114-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24	11			ENST00000287394.5:c.2792A>G	p.Lys931Arg	p.K931R	ENST00000287394	NM_014109.3	931	aAa/aGa	0	0.274	TTCAAAAAATTTTGTCCGTTC
HDX	139324	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	83724060	83724060	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-HT-8114-01	TCGA-HT-8114-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	86	10			ENST00000297977.5:c.671C>A	p.Pro224Gln	p.P224Q	ENST00000297977	NM_001177479.1	224	cCa/cAa	0	0.413	AATCCCAACTGGTTCAATTTT
RP11-248G5.8		broad.mit.edu;ucsc.edu	GRCh37	13	52865661	52865661	+	non_coding_transcript_exon_variant	RNA	SNP	C	C	A			TCGA-HT-8114-01	TCGA-HT-8114-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17	4			ENST00000451298.1:n.32G>T		*11*	ENST00000451298				0	0.289	AAGGATGACACAATTGAATGA
ATRX	546	broad.mit.edu;hgsc.bcm.edu	GRCh37	X	76937602	76937603	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T			TCGA-HT-8114-01	TCGA-HT-8114-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	46	36			ENST00000373344.5:c.3145dupA	p.Ile1049AsnfsTer4	p.I1049Nfs*4	ENST00000373344	NM_000489.3	1049	ata/aAta	0	0.327	TTTATCTCTTATTTTTTTACTT
ATRX	546	broad.mit.edu	GRCh37	X	76938089	76938092	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	rs141180098		TCGA-HT-8114-01	TCGA-HT-8114-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	208	25			ENST00000373344.5:c.2656_2659delGAGA	p.Glu886LeufsTer18	p.E886Lfs*18	ENST00000373344	NM_000489.3	886	GAGAct/ct	0	0.412	GAAGAGAAAGTCTCTCTCTCTTGT
PAPOLA	10914	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	14	97031339	97031339	+	missense_variant	Missense_Mutation	SNP	T	T	G			TCGA-HT-7610-01	TCGA-HT-7610-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	77	33			ENST00000216277.8:c.2190T>G	p.Asn730Lys	p.N730K	ENST00000216277	NM_032632.4	730	aaT/aaG	0	0.373	TCCCTGCAAATCCTATTCCTG
HBZ	3050	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	202926	202926	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-HT-7610-01	TCGA-HT-7610-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	53	24			ENST00000252951.2:c.18T>C	p.Thr6=	p.T6=	ENST00000252951	NM_005332.2	6	acT/acC	0	0.612	TGACCAAGACTGAGAGGACCA
SENP3	26168	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7474041	7474041	+	stop_gained	Nonsense_Mutation	SNP	C	C	T			TCGA-HT-7610-01	TCGA-HT-7610-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23	8			ENST00000429205.2:c.1522C>T	p.Arg508Ter	p.R508*	ENST00000429205		508	Cga/Tga	0	0.473	AAAGAAAGACCGACTGGATTT
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7577593	7577593	+	missense_variant	Missense_Mutation	SNP	T	T	G			TCGA-HT-7610-01	TCGA-HT-7610-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	63	21			ENST00000269305.4:c.688A>C	p.Thr230Pro	p.T230P	ENST00000269305	NM_001126112.2	230	Acc/Ccc	0	0.532	TGGATGGTGGTACAGTCAGAG
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7578507	7578507	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-HT-7610-01	TCGA-HT-7610-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30	32			ENST00000269305.4:c.423C>G	p.Cys141Trp	p.C141W	ENST00000269305	NM_001126112.2	141	tgC/tgG	0	0.577	GCTGCACAGGGCAGGTCTTGG
KRT27	342574	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	38936093	38936093	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7610-01	TCGA-HT-7610-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42	13			ENST00000301656.3:c.705C>T	p.Cys235=	p.C235=	ENST00000301656	NM_181537.3	235	tgC/tgT	0	0.483	CTCCAGCCGCGCACTGAAGAG
ABCG5	64240	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	44047075	44047075	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7610-01	TCGA-HT-7610-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	114	21			ENST00000260645.1:c.1628T>C	p.Leu543Pro	p.L543P	ENST00000260645	NM_022436.2	543	cTt/cCt	0	0.368	AGATCCAACAAGCACCCCCGC
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HT-7610-01	TCGA-HT-7610-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	83	32			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
TRIP12	9320	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	230668911	230668911	+	stop_gained	Nonsense_Mutation	SNP	G	G	A			TCGA-HT-7610-01	TCGA-HT-7610-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75	34			ENST00000283943.5:c.2458C>T	p.Arg820Ter	p.R820*	ENST00000283943	NM_004238.1	820	Cga/Tga	0	0.363	AGCTGTGCTCGAGCATCATCC
ASTE1	28990	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	130732931	130732931	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-7610-01	TCGA-HT-7610-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	72	14			ENST00000264992.3:c.2010G>A	p.Glu670=	p.E670=	ENST00000264992	NM_014065.2	670	gaG/gaA	0	0.393	CACTATGTTCCTCTAAGTTTT
LPHN3	23284	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	62813869	62813869	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7610-01	TCGA-HT-7610-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	27	7			ENST00000514591.1:c.2476C>T	p.Arg826Cys	p.R826C	ENST00000514591		826	Cgt/Tgt	0	0.388	CTACTCCAAGCGTACAATGAC
GPR124	25960	hgsc.bcm.edu;broad.mit.edu	GRCh37	8	37698691	37698691	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-7610-01	TCGA-HT-7610-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	94	11			ENST00000412232.2:c.2835C>T	p.Cys945=	p.C945=	ENST00000412232	NM_032777.9	945	tgC/tgT	0	0.627	ATTTCCTGTGCGCCGGGCTAC
SLC26A7	115111	hgsc.bcm.edu;ucsc.edu	GRCh37	8	92364100	92364100	+	synonymous_variant	Silent	SNP	T	T	G	rs10109254	byFrequency	TCGA-HT-7610-01	TCGA-HT-7610-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	125	36			ENST00000309536.2:c.1203T>G	p.Leu401=	p.L401=	ENST00000309536	NM_134266.1	401	ctT/ctG	0	0.343	GACCTTTGCTTTACTGGCTGC
ATRX	546	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	76890083	76890083	+	splice_donor_variant	Splice_Site	SNP	A	A	C			TCGA-HT-7610-01	TCGA-HT-7610-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74	38			ENST00000373344.5:c.4809+2T>G		p.X1603_splice	ENST00000373344	NM_000489.3			0	0.398	TTCAGCTCTTACCTGTAAAGT
STAG2	10735	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	123196967	123196967	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T			TCGA-HT-7610-01	TCGA-HT-7610-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	22	12			ENST00000218089.9:c.1733A>T	p.Tyr578Phe	p.Y578F	ENST00000218089	NM_001042749.1	578	tAc/tTc	0	0.313	ATTTCACAGTACTCTGTAGAT
BCOR	54880	broad.mit.edu;ucsc.edu	GRCh37	X	39931690	39931690	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7610-01	TCGA-HT-7610-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24	4			ENST00000378444.4:c.2909C>T	p.Ala970Val	p.A970V	ENST00000378444	NM_001123385.1	970	gCg/gTg	0	0.527	CACGTAACCCGCTGAGTTGGC
F5	2153	broad.mit.edu;ucsc.edu	GRCh37	1	169519050	169519050	+	stop_gained	Nonsense_Mutation	SNP	G	G	A			TCGA-HT-7610-01	TCGA-HT-7610-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36	4			ENST00000367797.3:c.1600C>T	p.Gln534Ter	p.Q534*	ENST00000367797	NM_000130.4	534	Caa/Taa	0	0.428	TGTATTCCTTGCCTGTCCAGG
OR8I2	120586	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	55860898	55860898	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-E1-5303-01	TCGA-E1-5303-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	330	159			ENST00000302124.2:c.115G>C	p.Val39Leu	p.V39L	ENST00000302124	NM_001003750.1	39	Gtt/Ctt	0	0.378	TCTATTCACTGTTTTGGGAAA
KIAA1377	57562	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	101818852	101818852	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-E1-5303-01	TCGA-E1-5303-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	77	46			ENST00000263468.8:c.485G>A	p.Arg162His	p.R162H	ENST00000263468	NM_020802.2	162	cGt/cAt	0	0.348	CCCTTTTCCCGTAGACCAACA
ARID2	196528	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	46242662	46242662	+	stop_gained	Nonsense_Mutation	SNP	C	C	T			TCGA-E1-5303-01	TCGA-E1-5303-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96	46			ENST00000334344.6:c.1624C>T	p.Arg542Ter	p.R542*	ENST00000334344	NM_152641.2	542	Cga/Tga	0	0.343	TTCTGTTTCTCGAGCAGAAAT
MED13L	23389	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	116460278	116460278	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-E1-5303-01	TCGA-E1-5303-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	38	15			ENST00000281928.3:c.608C>T	p.Ser203Leu	p.S203L	ENST00000281928	NM_015335.4	203	tCa/tTa	0	0.473	TGGTGCAGGTGAAGACTGAGC
OR11H4	390442	hgsc.bcm.edu;broad.mit.edu	GRCh37	14	20710969	20710969	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-E1-5303-01	TCGA-E1-5303-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	103	5			ENST00000315409.2:c.19G>C	p.Asp7His	p.D7H	ENST00000315409	NM_001004479.1	7	Gac/Cac	0	0.418	CTTCTTTGTAGACTTAAGACC
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660		TCGA-E1-5303-01	TCGA-E1-5303-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	20	64			ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	0	0.542	GCGCCGGTCTCTCCCAGGACA
SRCIN1	80725	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	36714502	36714502	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-E1-5303-01	TCGA-E1-5303-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	55	42			ENST00000264659.7:c.2162G>A	p.Arg721His	p.R721H	ENST00000264659	NM_025248.2	721	cGc/cAc	0	0.701	GTTGAGATAGCGCAGCCGTTC
EMILIN2	84034	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	18	2913269	2913269	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-E1-5303-01	TCGA-E1-5303-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62	32			ENST00000254528.3:c.3029T>C	p.Leu1010Pro	p.L1010P	ENST00000254528	NM_032048.2	1010	cTc/cCc	0	0.592	GCATTCCACCTCATCGTGCAC
FZR1	51343	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	3532532	3532532	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-E1-5303-01	TCGA-E1-5303-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	56	7			ENST00000395095.3:c.1126G>C	p.Gly376Arg	p.G376R	ENST00000395095	NM_001136198.1	376	Ggc/Cgc	0	0.652	CTCGGGGGGCGGCACAGCTGA
PLA2G4A	5321	hgsc.bcm.edu;broad.mit.edu	GRCh37	1	186948459	186948459	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-E1-5303-01	TCGA-E1-5303-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	150	8			ENST00000367466.3:c.1973A>G	p.Glu658Gly	p.E658G	ENST00000367466	NM_024420.2	658	gAa/gGa	0	0.333	GTTCCAAGGGAAACTGAGGAA
CHD6	84181	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	20	40045243	40045243	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-E1-5303-01	TCGA-E1-5303-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	190	86			ENST00000373233.3:c.6471G>A	p.Ala2157=	p.A2157=	ENST00000373233	NM_032221.4	2157	gcG/gcA	0	0.552	GGATCTGGGCCGCCAATGCTG
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	179456089	179456089	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-E1-5303-01	TCGA-E1-5303-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	593	284			ENST00000589042.1:c.60363C>T	p.Thr20121=	p.T20121=	ENST00000589042	NM_001267550.1	20121	acC/acT	0	0.433	AGTGCTCATCGGTTTTAATCT
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-E1-5303-01	TCGA-E1-5303-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	108	46			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
SLC23A3	151295	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	220034279	220034279	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-E1-5303-01	TCGA-E1-5303-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	269	101			ENST00000455516.2:c.284G>A	p.Gly95Asp	p.G95D	ENST00000455516	NM_001144890.1	95	gGt/gAt	0	0.582	GGTAGACATACCACATGAAAA
SENP7	57337	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	101177814	101177814	+	missense_variant	Missense_Mutation	SNP	T	T	G			TCGA-E1-5303-01	TCGA-E1-5303-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	433	87			ENST00000394095.2:c.269A>C	p.Lys90Thr	p.K90T	ENST00000394095	NM_020654.3	90	aAg/aCg	0	0.358	TGGTGATGACTTGGAAGTAAC
ZMAT3	64393	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	178748788	178748788	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G			TCGA-E1-5303-01	TCGA-E1-5303-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	77	44			ENST00000311417.2:c.271-1G>C		p.X91_splice	ENST00000311417	NM_022470.3			0	0.398	GATTTTTACCCTAGAAATAAA
AFP	174	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	74303981	74303981	+	missense_variant	Missense_Mutation	SNP	A	A	C			TCGA-E1-5303-01	TCGA-E1-5303-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	121	23			ENST00000395792.2:c.228A>C	p.Lys76Asn	p.K76N	ENST00000395792	NM_001134.1	76	aaA/aaC	0	0.363	CAATTGAGAAACCCACTggag
SPZ1	84654	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	79616896	79616896	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-E1-5303-01	TCGA-E1-5303-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	130	71			ENST00000296739.4:c.862G>A	p.Gly288Ser	p.G288S	ENST00000296739	NM_032567.3	288	Ggt/Agt	0	0.413	TAATGGAGTCGGTTTCCAAAC
GPR98	84059	hgsc.bcm.edu;ucsc.edu	GRCh37	5	89914934	89914934	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-E1-5303-01	TCGA-E1-5303-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	27	5			ENST00000405460.2:c.389C>A	p.Pro130Gln	p.P130Q	ENST00000405460	NM_032119.3	130	cCa/cAa	0	0.259	CTTGGATGGCCAAGGACTGTT
TRIM52	84851	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	180687093	180687093	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-E1-5303-01	TCGA-E1-5303-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	171	108			ENST00000327767.4:c.722A>G	p.Asp241Gly	p.D241G	ENST00000327767	NM_032765.2	241	gAc/gGc	0	0.542	GGCCTCTTTGTCCACCTCACA
UTRN	7402	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	144872125	144872125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs114254210	byFrequency	TCGA-E1-5303-01	TCGA-E1-5303-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	116	46			ENST00000367545.3:c.6835C>T	p.Arg2279Cys	p.R2279C	ENST00000367545	NM_007124.2	2279	Cgc/Tgc	0	0.338	CTTAGAACAGCGCCATCCTCA
COG5	10466	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	107002756	107002756	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-E1-5303-01	TCGA-E1-5303-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91	12			ENST00000297135.3:c.1038A>G	p.Gly346=	p.G346=	ENST00000297135	NM_006348.3	346	ggA/ggG	0	0.393	TATTTACCTGTCCACAAACAG
AGK	55750	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	141301025	141301025	+	missense_variant	Missense_Mutation	SNP	A	A	C			TCGA-E1-5303-01	TCGA-E1-5303-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	154	25			ENST00000355413.4:c.242A>C	p.Glu81Ala	p.E81A	ENST00000355413	NM_018238.3	81	gAa/gCa	0	0.363	ACTCTATTTGAAAAAAATGCT
KCNV1	27012	hgsc.bcm.edu;broad.mit.edu	GRCh37	8	110984685	110984685	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-E1-5303-01	TCGA-E1-5303-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	181	12			ENST00000524391.1:c.793C>T	p.Arg265Trp	p.R265W	ENST00000524391		265	Cgg/Tgg	0	0.532	CACCTGTCCCGCACACACAGG
C9orf114	51490	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	131586077	131586077	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-E1-5303-01	TCGA-E1-5303-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10	4			ENST00000361256.5:c.1011C>G	p.Asp337Glu	p.D337E	ENST00000361256	NM_016390.3	337	gaC/gaG	0	0.642	TGACGTACAGGTCAAAGAGGA
ZFX	7543	hgsc.bcm.edu;broad.mit.edu	GRCh37	X	24229263	24229263	+	stop_gained	Nonsense_Mutation	SNP	C	C	T			TCGA-E1-5303-01	TCGA-E1-5303-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	181	11			ENST00000379177.1:c.2188C>T	p.Gln730Ter	p.Q730*	ENST00000379177	NM_003410.3	730	Caa/Taa	0	0.408	GGGATTTAGGCAACAGAGTGA
HEATR2	54919	broad.mit.edu;ucsc.edu	GRCh37	7	813720	813720	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-E1-5303-01	TCGA-E1-5303-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	158	56			ENST00000297440.6:c.1967A>G	p.Asp656Gly	p.D656G	ENST00000297440	NM_017802.3	656	gAc/gGc	0	0.642	GTGACAAAGGACATCCTGGCC
ATRX	546	broad.mit.edu;hgsc.bcm.edu	GRCh37	X	76939929	76939930	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A			TCGA-E1-5303-01	TCGA-E1-5303-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	123	232			ENST00000373344.5:c.818dupT	p.Leu273PhefsTer9	p.L273Ffs*9	ENST00000373344	NM_000489.3	273	ttg/ttTg	0	0.381	CCAAGTCCAACAAAGGCTCTGG
KIAA1462	57608	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	30316584	30316584	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-HT-7482-01	TCGA-HT-7482-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	106	15			ENST00000375377.1:c.2493G>C	p.Leu831Phe	p.L831F	ENST00000375377	NM_020848.2	831	ttG/ttC	0	0.557	ACTGACTGATCAAATCCCAGG
BRSK2	9024	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	1477653	1477653	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7482-01	TCGA-HT-7482-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11	9			ENST00000382179.1:c.1882G>A	p.Val628Met	p.V628M	ENST00000382179	NM_001256630.1	628	Gtg/Atg	0	0.612	GGGGCCAGCCGTGTTCCAGAA
SLC6A15	55117	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	85255483	85255483	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-HT-7482-01	TCGA-HT-7482-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	129	9			ENST00000266682.5:c.2121T>C	p.Ala707=	p.A707=	ENST00000266682	NM_182767.5	707	gcT/gcC	0	0.423	GTCCATTGGGAGCAGTATCCA
SRL	6345	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	4242361	4242361	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7482-01	TCGA-HT-7482-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39	25			ENST00000399609.3:c.1215C>T	p.Phe405=	p.F405=	ENST00000399609	NM_001098814.1	405	ttC/ttT	0	0.493	GATTGATGCCGAAGAAGTCCT
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137852790		TCGA-HT-7482-01	TCGA-HT-7482-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29	17			ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	0	0.612	GGTGCCGGGCGGGGGTGTGGA
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499		TCGA-HT-7482-01	TCGA-HT-7482-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	53	19			ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	0	0.398	TAAGCATGACGACCTATGATG
DPPA4	55211	hgsc.bcm.edu;broad.mit.edu	GRCh37	3	109049418	109049418	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-HT-7482-01	TCGA-HT-7482-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57	5			ENST00000335658.6:c.632C>G	p.Ala211Gly	p.A211G	ENST00000335658	NM_018189.3	211	gCc/gGc	0	0.522	CCTCGCCCTGGCTGAAATTCT
PLXNA1	5361	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	126732904	126732904	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-HT-7482-01	TCGA-HT-7482-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	120	28			ENST00000393409.2:c.2355C>G	p.Asn785Lys	p.N785K	ENST00000393409	NM_032242.3	785	aaC/aaG	0	0.632	TGCCAGTGAACCTGTCAGTCG
KHDRBS2	202559	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	62611243	62611243	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7482-01	TCGA-HT-7482-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26	17			ENST00000281156.4:c.517C>T	p.Arg173Cys	p.R173C	ENST00000281156	NM_152688.2	173	Cgt/Tgt	0	0.418	GATAATTCACGTAGTTGTTCC
SLC2A12	154091	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	134350799	134350799	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-HT-7482-01	TCGA-HT-7482-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	34	6			ENST00000275230.5:c.164G>C	p.Gly55Ala	p.G55A	ENST00000275230	NM_145176.2	55	gGt/gCt	0	0.517	AAGTTCATAACCCACCAGGAG
VPS41	27072	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	38796519	38796519	+	synonymous_variant	Silent	SNP	G	G	A	rs146405914		TCGA-HT-7482-01	TCGA-HT-7482-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	22	10			ENST00000310301.4:c.1614C>T	p.Asp538=	p.D538=	ENST00000310301	NM_014396.3	538	gaC/gaT	0	0.284	ACTGAAAAACGTCTTTATGTC
MET	4233	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	116381017	116381017	+	stop_gained	Nonsense_Mutation	SNP	C	C	T			TCGA-HT-7482-01	TCGA-HT-7482-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	86	20			ENST00000397752.3:c.1639C>T	p.Arg547Ter	p.R547*	ENST00000397752	NM_000245.2	547	Cga/Tga	0	0.512	CAAATGTGTGCGATCGGAGGA
AKR1B15	441282	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	134256364	134256364	+	missense_variant	Missense_Mutation	SNP	T	T	A			TCGA-HT-7482-01	TCGA-HT-7482-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74	13			ENST00000457545.2:c.444T>A	p.Asp148Glu	p.D148E	ENST00000457545	NM_001080538.2	148	gaT/gaA	0	0.423	AGACTGGGGATGACTTTTTCC
ATRX	546	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	76849221	76849221	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7482-01	TCGA-HT-7482-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62	20			ENST00000373344.5:c.6055A>G	p.Lys2019Glu	p.K2019E	ENST00000373344	NM_000489.3	2019	Aaa/Gaa	0	0.363	AGTACCATTTTCCCAGAATGC
RBM41	55285	broad.mit.edu;ucsc.edu	GRCh37	X	106310757	106310757	+	stop_lost	Nonstop_Mutation	SNP	C	C	A			TCGA-HT-7482-01	TCGA-HT-7482-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	161	43			ENST00000372479.3:c.1242G>T	p.Ter414TyrextTer13	p.*414Yext*13	ENST00000372479	NM_018301.3	414	taG/taT	0	0.378	TATATATATTCTAGCTACCAC
TP53	7157	broad.mit.edu;ucsc.edu	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343		TCGA-HT-7482-01	TCGA-HT-7482-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	19	8			ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	0	0.542	GCACAAACACGCACCTCAAAG
ANKRD1	27063	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	92678671	92678671	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18	19			ENST00000371697.3:c.404T>C	p.Val135Ala	p.V135A	ENST00000371697	NM_014391.2	135	gTa/gCa	0	0.343	TTTTTCTACTACTGGCAGTTT
TMEM180	79847	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	104233397	104233397	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	22	31			ENST00000238936.4:c.996C>T	p.Tyr332=	p.Y332=	ENST00000238936	NM_024789.3	332	taC/taT	0	0.637	GGGGCGTCTACGCGGTGGTGC
TACC2	10579	hgsc.bcm.edu;broad.mit.edu	GRCh37	10	123844064	123844064	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2	4			ENST00000369005.1:c.2049C>T	p.Pro683=	p.P683=	ENST00000369005	NM_206862.2	683	ccC/ccT	0	0.582	CCACTGTTCCCGAAGGAGCCA
MUC5B	727897	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	1271606	1271606	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91	60			ENST00000529681.1:c.13496C>T	p.Ser4499Phe	p.S4499F	ENST00000529681	NM_002458.2	4499	tCc/tTc	0	0.642	ACTCCCTCCTCCAGTCCAGGG
OR5F1	338674	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	55761801	55761801	+	missense_variant	Missense_Mutation	SNP	T	T	A			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64	32			ENST00000278409.1:c.301A>T	p.Met101Leu	p.M101L	ENST00000278409	NM_003697.1	101	Atg/Ttg	0	0.463	AAGAAGTACATCTGTAGGAAG
PDE2A	5138	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	72289381	72289381	+	splice_region_variant,synonymous_variant	Splice_Region	SNP	C	C	T			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	38	27			ENST00000334456.5:c.2511G>A	p.Glu837=	p.E837=	ENST00000334456	NM_002599.4	837	gaG/gaA	0	0.582	CCATGGCCTTCTCCTGCAGGC
OR2AT4	341152	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	74800020	74800020	+	missense_variant	Missense_Mutation	SNP	T	T	A			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15	11			ENST00000305159.3:c.739A>T	p.Ser247Cys	p.S247C	ENST00000305159	NM_001005285.1	247	Agc/Tgc	0	0.567	AGGTGGGAGCTGCAGGTGGAG
ACSM4	341392	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	7477158	7477158	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36	15			ENST00000399422.4:c.1500G>A	p.Ser500=	p.S500=	ENST00000399422	NM_001080454.1	500	tcG/tcA	0	0.428	TTGTTGAATCGGCTGTTGTCA
GUCY2C	2984	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	14809526	14809526	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42	25			ENST00000261170.3:c.1390C>T	p.Arg464Cys	p.R464C	ENST00000261170	NM_004963.3	464	Cgt/Tgt	0	0.373	TTTTTCTGACGAAGTTCATAA
ALG5	29880	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	13	37569684	37569684	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42	15			ENST00000239891.3:c.116G>A	p.Arg39Gln	p.R39Q	ENST00000239891	NM_013338.4	39	cGa/cAa	0	0.383	TTCTTCATGTCGATGGAGTGC
SYNE3	161176	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	14	95932397	95932397	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35	23			ENST00000334258.5:c.498G>A	p.Gln166=	p.Q166=	ENST00000334258	NM_152592.3	166	caG/caA	0	0.637	GGAGCACCGCCTGGTTGTCCA
ATP8B4	79895	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	50223421	50223421	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26	17			ENST00000284509.6:c.1537C>T	p.Arg513Trp	p.R513W	ENST00000284509	NM_024837.3	513	Cgg/Tgg	0	0.398	TCTGGGGTCCGGGATTTAAAA
MYO5A	4644	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	52622646	52622646	+	stop_gained	Nonsense_Mutation	SNP	G	G	A			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75	56			ENST00000399231.3:c.4384C>T	p.Arg1462Ter	p.R1462*	ENST00000399231	NM_000259.3	1462	Cga/Tga	0	0.413	TTGACTGGTCGGATGGGTTCA
OR4F6	390648	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	102346763	102346763	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29	23			ENST00000328882.4:c.841G>A	p.Val281Ile	p.V281I	ENST00000328882	NM_001005326.1	281	Gtt/Att	0	0.343	TATCACTCCCGTTTTGAATCC
SPNS1	83985	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	28995597	28995597	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21	9			ENST00000311008.11:c.1564C>T	p.Pro522Ser	p.P522S	ENST00000311008	NM_032038.2	522	Ccc/Tcc	0	0.697	CACCCGCGTGCCCGTGGCCAG
CHST4	10164	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	71570880	71570880	+	synonymous_variant	Silent	SNP	C	C	T	rs139260372		TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37	22			ENST00000338482.5:c.300C>T	p.Ala100=	p.A100=	ENST00000338482		100	gcC/gcT	0	0.582	TGATACGGGCCGTCTTCTTGT
ACLY	47	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	40040509	40040509	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28	20			ENST00000352035.2:c.2091C>G	p.Phe697Leu	p.F697L	ENST00000352035	NM_001096.2	697	ttC/ttG	0	0.438	CATGATCCATGAATGTGGAGC
EPN3	55040	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	48616618	48616618	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	32	18			ENST00000268933.3:c.833G>A	p.Arg278Gln	p.R278Q	ENST00000268933	NM_017957.2	278	cGg/cAg	0	0.597	CACCATCAGCGGGACAGAGAG
CATSPERD	257062	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	5727283	5727283	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75	29			ENST00000381624.3:c.131G>A	p.Arg44His	p.R44H	ENST00000381624	NM_152784.3	44	cGc/cAc	0	0.338	CTCTAGGACCGCCTGTATTTT
SLC8A2	6543	hgsc.bcm.edu;ucsc.edu	GRCh37	19	47935494	47935494	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	59	11			ENST00000236877.6:c.2319C>T	p.Phe773=	p.F773=	ENST00000236877	NM_015063.2	773	ttC/ttT	0	0.627	CGGTGCAGCCGAAGTGGGAGG
MYH14	79784	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	50750373	50750373	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21	8			ENST00000601313.1:c.1323G>A	p.Lys441=	p.K441=	ENST00000601313	NM_001145809.1	441	aaG/aaA	0	0.597	CCCAGACTAAGGAACAGGTAG
SELE	6401	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	169698637	169698637	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36	39			ENST00000333360.7:c.893C>T	p.Thr298Met	p.T298M	ENST00000333360	NM_000450.2	298	aCg/aTg	0	0.443	ACCTTTACACGTTGGCTTCTC
VSX1	30813	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	20	25057044	25057044	+	synonymous_variant	Silent	SNP	A	A	C			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64	34			ENST00000376709.4:c.951T>G	p.Pro317=	p.P317=	ENST00000376709	NM_014588.5	317	ccT/ccG	0	0.542	AGCCATTCTCAGGGCTCACTT
GREB1	9687	hgsc.bcm.edu;broad.mit.edu	GRCh37	2	11725320	11725320	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14	14			ENST00000381486.2:c.935G>A	p.Arg312His	p.R312H	ENST00000381486	NM_014668.3	312	cGc/cAc	0	0.512	CCCAAAAAACGCCACAAAGGG
CENPA	1058	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	27016113	27016113	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	134	61			ENST00000335756.4:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000335756	NM_001809.3	130	cGg/cAg	0	0.552	CAACTGGCCCGGAGGATCCGG
G6PC2	57818	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	169764413	169764413	+	missense_variant	Missense_Mutation	SNP	T	T	G			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78	43			ENST00000375363.3:c.892T>G	p.Leu298Val	p.L298V	ENST00000375363	NM_021176.2	298	Ttg/Gtg	0	0.473	GCTCTGTGCCTTGACCTCATT
GPR55	9290	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	231774733	231774733	+	synonymous_variant	Silent	SNP	C	C	T	rs146835586		TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42	33			ENST00000392040.1:c.945G>A	p.Thr315=	p.T315=	ENST00000392040	NM_005683.3	315	acG/acA	0	0.552	CCCGGGAGATCGTGGTGTCCT
COL6A3	1293	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	238275437	238275437	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52	31			ENST00000295550.4:c.5393G>A	p.Arg1798His	p.R1798H	ENST00000295550	NM_004369.3	1798	cGc/cAc	0	0.547	GTTGCCCACGCGGAACGCTGT
GPR98	84059	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	90136725	90136725	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	25	16			ENST00000405460.2:c.16942C>T	p.Leu5648Phe	p.L5648F	ENST00000405460	NM_032119.3	5648	Ctc/Ttc	0	0.423	CAACAGAGTGCTCCATACCAT
PCDH12	51294	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	141335542	141335542	+	missense_variant	Missense_Mutation	SNP	A	A	T			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15	9			ENST00000231484.3:c.1875T>A	p.Asp625Glu	p.D625E	ENST00000231484	NM_016580.3	625	gaT/gaA	0	0.582	CCGAGTCTGCATCTCTTGCCA
SH3TC2	79628	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	148411245	148411245	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17	17			ENST00000515425.1:c.1007G>A	p.Arg336Lys	p.R336K	ENST00000515425	NM_024577.3	336	aGg/aAg	0	0.522	GGCAGAGTTCCTGCTCCTGCA
GRIA1	2890	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	153056693	153056693	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15	5			ENST00000518783.1:c.1031G>A	p.Gly344Glu	p.G344E	ENST00000518783	NM_001258021.1	344	gGg/gAg	0	0.537	TGGGGCCAAGGGATCGACATC
TENM2	57451	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	167671581	167671581	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39	28			ENST00000518659.1:c.5677G>A	p.Val1893Met	p.V1893M	ENST00000518659	NM_001122679.1	1893	Gtg/Atg	0	0.597	AGCTGTCAACGTGTCATACTT
GABRP	2568	hgsc.bcm.edu;ucsc.edu	GRCh37	5	170232777	170232777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs112704076	byFrequency	TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23	22			ENST00000518525.1:c.599G>A	p.Arg200His	p.R200H	ENST00000518525		200	cGt/cAt	0	0.522	GACTCTGTGCGTGGACTGGAA
HLA-DMB	3109	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	32906668	32906668	+	missense_variant	Missense_Mutation	SNP	T	T	G			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	54	21			ENST00000418107.2:c.130A>C	p.Ile44Leu	p.I44L	ENST00000418107	NM_002118.4	44	Atc/Ctc	0	0.527	TTGAAGGAGATGCAGTATGTG
LAMA4	3910	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	112469437	112469437	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7	29			ENST00000230538.7:c.2275C>G	p.Leu759Val	p.L759V	ENST00000230538	NM_001105206.2	759	Cta/Gta	0	0.517	CAGTTGGTTAGATTGTTGGCC
TCTE3	6991	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	170144257	170144257	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26	18			ENST00000366774.3:c.234G>A	p.Leu78=	p.L78=	ENST00000366774	NM_174910.1	78	ctG/ctA	0	0.373	TTAATTTTGCCAGGGCACTCT
DYNC1I1	1780	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	95657632	95657632	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58	27			ENST00000324972.6:c.1166C>T	p.Thr389Met	p.T389M	ENST00000324972	NM_004411.4	389	aCg/aTg	0	0.493	GCTGCACACACGGTAATGCAA
LAMB1	3912	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	107616242	107616242	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61	25			ENST00000222399.6:c.1081G>A	p.Val361Met	p.V361M	ENST00000222399	NM_002291.2	361	Gtg/Atg	0	0.517	TCATCACACACGCCTCCGCTG
DOCK5	80005	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	25198440	25198440	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9	9			ENST00000276440.7:c.2375G>A	p.Arg792His	p.R792H	ENST00000276440	NM_024940.6	792	cGc/cAc	0	0.398	AATTCAATTCGCCAGTTATTT
ASAP1	50807	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	131149272	131149272	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	43	31			ENST00000357668.1:c.1093C>A	p.Pro365Thr	p.P365T	ENST00000357668		365	Cca/Aca	0	0.448	AACTTGGCTGGTTGCCTGTTA
MAMDC2	256691	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	72724721	72724721	+	splice_donor_variant	Splice_Site	SNP	G	G	A			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52	48			ENST00000377182.4:c.505+1G>A		p.X169_splice	ENST00000377182	NM_153267.4			0	0.368	TACTGTATTGGTAAGTGGGCT
GOLGA2	2801	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	131022430	131022430	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	51	35			ENST00000421699.2:c.1716G>A	p.Ser572=	p.S572=	ENST00000421699	NM_004486.4	572	tcG/tcA	0	0.592	CGTGCTGCTCCGACTGCAGTG
FAM47B	170062	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	34961315	34961315	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	19	33			ENST00000329357.5:c.367G>T	p.Ala123Ser	p.A123S	ENST00000329357	NM_152631.2	123	Gcc/Tcc	0	0.537	GGAAGTGGAAGCCCAGCTGAT
MAGEB16	139604	hgsc.bcm.edu;broad.mit.edu	GRCh37	X	35820491	35820491	+	missense_variant	Missense_Mutation	SNP	A	A	T			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1	9			ENST00000399989.1:c.178A>T	p.Ser60Cys	p.S60C	ENST00000399989	NM_001099921.1	60	Agt/Tgt	0	0.532	TAAGGCAGAGAGTCCTCTTGA
DDX26B	203522	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	134706886	134706886	+	synonymous_variant	Silent	SNP	G	G	T			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9	30			ENST00000370752.4:c.1434G>T	p.Gly478=	p.G478=	ENST00000370752	NM_182540.4	478	ggG/ggT	0	0.353	AAATCACAGGGGAAACTGCAC
SPANXN2	494119	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	142795437	142795437	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	17	141			ENST00000370498.1:c.241G>A	p.Val81Ile	p.V81I	ENST00000370498	NM_001009615.1	81	Gtc/Atc	0	0.453	TCCTCTTGGACGGGATTGATG
SLC23A2	9962	broad.mit.edu;ucsc.edu	GRCh37	20	4850643	4850643	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	51	27			ENST00000379333.1:c.1159G>A	p.Val387Met	p.V387M	ENST00000379333	NM_203327.1	387	Gtg/Atg	0	0.602	CTGGCGACCACGGCACTGAGC
OR1N1	138883	broad.mit.edu;ucsc.edu	GRCh37	9	125289214	125289214	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29	4			ENST00000304880.2:c.359G>A	p.Arg120His	p.R120H	ENST00000304880	NM_012363.1	120	cGc/cAc	0	0.512	GGCCACATAGCGGTCATACGC
HOXB5	3215	broad.mit.edu;ucsc.edu	GRCh37	17	46670842	46670842	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15	5			ENST00000239151.5:c.203C>T	p.Ala68Val	p.A68V	ENST00000239151	NM_002147.3	68	gCg/gTg	0	0.687	CTCGCCCACCGCCCCAAAGTG
COL1A1	1277	broad.mit.edu;ucsc.edu	GRCh37	17	48270361	48270361	+	synonymous_variant	Silent	SNP	G	G	A	rs72651616		TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	16	5			ENST00000225964.5:c.1815C>T	p.Gly605=	p.G605=	ENST00000225964	NM_000088.3	605	ggC/ggT	0	0.627	TTACGACAGCGCCAGGGGGTC
TTC21A	199223	broad.mit.edu;ucsc.edu	GRCh37	3	39179140	39179140	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	13	3			ENST00000431162.2:c.3635G>C	p.Cys1212Ser	p.C1212S	ENST00000431162		1212	tGc/tCc	0	0.607	GACATTTACTGCCAGGGCAGC
FCHSD1	89848	broad.mit.edu;ucsc.edu	GRCh37	5	141028985	141028985	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	151	73			ENST00000435817.2:c.352G>A	p.Ala118Thr	p.A118T	ENST00000435817	NM_033449.2	118	Gcc/Acc	0	0.612	TGCTCCTTGGCGCTCCGCCCT
KCNS3	3790	broad.mit.edu;ucsc.edu	GRCh37	2	18113040	18113040	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	51	37			ENST00000403915.1:c.765G>A	p.Leu255=	p.L255=	ENST00000403915	NM_001282428.1	255	ctG/ctA	0	0.512	AAAACCCTCTGAACATCATTG
ITPR1	3708	broad.mit.edu;ucsc.edu	GRCh37	3	4819013	4819013	+	synonymous_variant	Silent	SNP	C	C	A			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8	6			ENST00000302640.8:c.6201C>A	p.Ile2067=	p.I2067=	ENST00000302640	NM_001168272.1	2067	atC/atA	0	0.423	TCAATGATATCAATCCTTTGG
USH2A	7399	broad.mit.edu;ucsc.edu	GRCh37	1	216251647	216251647	+	stop_gained	Nonsense_Mutation	SNP	G	G	A			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	188	131			ENST00000307340.3:c.5356C>T	p.Gln1786Ter	p.Q1786*	ENST00000307340	NM_206933.2	1786	Caa/Taa	0	0.348	AGATCCACTTGTGTAAAGGCA
CACNA1S	779	broad.mit.edu;ucsc.edu	GRCh37	1	201047161	201047161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs9333651		TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	38	26			ENST00000362061.3:c.1465C>T	p.Arg489Cys	p.R489C	ENST00000362061	NM_000069.2	489	Cgc/Tgc	0	0.582	AAGTACTGGCGCAGGCCCAGC
NLRP9	338321	broad.mit.edu;ucsc.edu	GRCh37	19	56244617	56244617	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29	4			ENST00000332836.2:c.580G>A	p.Ala194Thr	p.A194T	ENST00000332836	NM_176820.2	194	Gca/Aca	0	0.453	CTGGTCTCTGCGATACCGTTC
SEC23B	10483	broad.mit.edu;ucsc.edu	GRCh37	20	18516372	18516372	+	stop_gained	Nonsense_Mutation	SNP	G	G	T			TCGA-CS-6186-01	TCGA-CS-6186-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	27	4			ENST00000336714.3:c.1390G>T	p.Glu464Ter	p.E464*	ENST00000336714	NM_032985.4	464	Gaa/Taa	0	0.433	CATCTATTTTGAAGTTGTCAA
PTEN	5728	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	89692835	89692835	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs57374291		TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	48	25			ENST00000371953.3:c.319G>T	p.Asp107Tyr	p.D107Y	ENST00000371953	NM_000314.4	107	Gat/Tat	0	0.368	CTTTTGTGAAGATCTTGACCA
MS4A6E	245802	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	60107365	60107365	+	synonymous_variant	Silent	SNP	T	T	A			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	200	76			ENST00000300182.4:c.381T>A	p.Ser127=	p.S127=	ENST00000300182	NM_139249.2	127	tcT/tcA	0	0.493	TGCTGGTTTCTACTGTGTTGG
EXPH5	23086	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	108381685	108381685	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30	8			ENST00000265843.4:c.4549C>A	p.Leu1517Ile	p.L1517I	ENST00000265843	NM_015065.2	1517	Cta/Ata	0	0.433	CCAAGCTGTAGTTTATGCAAT
EXPH5	23086	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	108382533	108382533	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99	24			ENST00000265843.4:c.3701C>G	p.Thr1234Arg	p.T1234R	ENST00000265843	NM_015065.2	1234	aCg/aGg	0	0.373	AACAGAAAACGTACTAGTCGT
FZD10	11211	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	130648631	130648631	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	43	18			ENST00000229030.4:c.1144G>A	p.Gly382Arg	p.G382R	ENST00000229030		382	Ggg/Agg	0	0.647	CGAGCTCACCGGGGTCTGCTA
TICRR	90381	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	90167424	90167424	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	94	43			ENST00000268138.7:c.3883C>A	p.Pro1295Thr	p.P1295T	ENST00000268138		1295	Cca/Aca	0	0.453	TCCAAAAAGACCAGGGAATTC
MYO15A	51168	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	18053797	18053797	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	44	10			ENST00000205890.5:c.7267G>A	p.Gly2423Ser	p.G2423S	ENST00000205890	NM_016239.3	2423	Ggt/Agt	0	0.617	AGGCCAGCCCGGTGGAGGCAG
NF1	4763	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	29663747	29663747	+	stop_gained	Nonsense_Mutation	SNP	T	T	G			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61	23			ENST00000358273.4:c.6242T>G	p.Leu2081Ter	p.L2081*	ENST00000358273	NM_001042492.2	2081	tTa/tGa	0	0.408	ATTGCTATTTTAGCACGCTAC
ANKRD30B	374860	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	18	14763803	14763803	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14	8			ENST00000358984.4:c.939G>A	p.Thr313=	p.T313=	ENST00000358984	NM_001145029.1	313	acG/acA	0	0.478	TGGAGGGAACGTCTGCCAAAA
NEDD4L	23327	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	18	56008358	56008358	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7	4			ENST00000400345.3:c.1214A>G	p.Asn405Ser	p.N405S	ENST00000400345	NM_001144967.2	405	aAt/aGt	0	0.478	TACTATGTCAATCATAACAAT
CD70	970	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	6590911	6590911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148772362		TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62	32			ENST00000245903.3:c.103G>A	p.Val35Met	p.V35M	ENST00000245903	NM_001252.3	35	Gtg/Atg	0	0.627	ATGCACACCACGAGGCAGATC
UBE2M	9040	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	59068093	59068093	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35	18			ENST00000253023.3:c.308A>G	p.Asn103Ser	p.N103S	ENST00000253023	NM_003969.3	103	aAc/aGc	0	0.582	GAGGTCAATGTTGGGGTGATA
PRAMEF4	400735	hgsc.bcm.edu;broad.mit.edu	GRCh37	1	12941802	12941802	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	239	83			ENST00000235349.5:c.748G>A	p.Val250Ile	p.V250I	ENST00000235349	NM_001009611.2	250	Gtt/Att	0	0.488	TCTGGGGAAACGTAGCGAGAG
TCHH	7062	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	152082385	152082385	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	48	22			ENST00000368804.1:c.3308G>A	p.Arg1103His	p.R1103H	ENST00000368804	NM_007113.3	1103	cGc/cAc	0	0.612	CCGCTCCTGGCGCCTTCTCTT
CD1E	913	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	158324220	158324220	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90	29			ENST00000368167.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000368167	NM_030893.3	38	Cgc/Tgc	0	0.542	GCTGTCCTTCCGCATGCTCCA
RYR2	6262	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	237777663	237777663	+	missense_variant	Missense_Mutation	SNP	A	A	T			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	22	12			ENST00000366574.2:c.5235A>T	p.Lys1745Asn	p.K1745N	ENST00000366574	NM_001035.2	1745	aaA/aaT	0	0.517	AGAACAAAAAACACGGCCTTC
PHACTR3	116154	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	20	58349322	58349322	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	34	14			ENST00000371015.1:c.951G>A	p.Gly317=	p.G317=	ENST00000371015	NM_080672.4	317	ggG/ggA	0	0.527	AAAGTAAAGGGTCTCCAAAGA
LRRC3	81543	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	21	45877263	45877263	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33	13			ENST00000291592.4:c.736G>A	p.Ala246Thr	p.A246T	ENST00000291592	NM_030891.3	246	Gcc/Acc	0	0.652	TCTGCCCAGCGCCCCCGCCTC
SFI1	9814	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	22	32013006	32013006	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs143349198	by1000genomes	TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	31	19			ENST00000400288.2:c.3454G>C	p.Glu1152Gln	p.E1152Q	ENST00000400288	NM_001007467.2	1152	Gaa/Caa	0	0.567	CCTTGAGGCTGAACTTGAGGA
DEPDC5	9681	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	22	32302244	32302244	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33	14			ENST00000382112.3:c.4546C>T	p.Arg1516Trp	p.R1516W	ENST00000382112	NM_001136029.2	1516	Cgg/Tgg	0	0.607	AGGGCAGCAGCGGCGGCGGCG
PDIA6	10130	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	10929977	10929977	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	65	24			ENST00000272227.3:c.738C>T	p.Gly246=	p.G246=	ENST00000272227	NM_005742.2	246	ggC/ggT	0	0.423	CAGGAGACTCGCCTTTCTGAA
KCNS3	3790	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	18113581	18113581	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69	34			ENST00000403915.1:c.1306C>A	p.Pro436Thr	p.P436T	ENST00000403915	NM_001282428.1	436	Cct/Act	0	0.453	TCATGAGCTACCTTACTTTAA
CLHC1	130162	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	55404777	55404777	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	48	17			ENST00000401408.1:c.1525G>C	p.Gly509Arg	p.G509R	ENST00000401408	NM_152385.2	509	Ggc/Cgc	0	0.353	AGCTTAATGCCAACTTTTTTC
B3GNT7	93010	hgsc.bcm.edu;broad.mit.edu	GRCh37	2	232263412	232263412	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39	18			ENST00000287590.5:c.982G>A	p.Val328Ile	p.V328I	ENST00000287590	NM_145236.2	328	Gtc/Atc	0	0.672	GATCGACGACGTCTTTCTGGG
GIGYF2	26058	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	233681681	233681681	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149585458		TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	108	67			ENST00000409451.3:c.2372G>A	p.Arg791Gln	p.R791Q	ENST00000409451		791	cGg/cAg	0	0.488	GAAATTCTTCGGCGACAGCAG
PROM1	8842	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	15991422	15991422	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7	6			ENST00000510224.1:c.2009T>C	p.Leu670Pro	p.L670P	ENST00000510224		670	cTg/cCg	0	0.413	ATCTCTTTTCAGGGAGTTCCT
CCKAR	886	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	26483467	26483467	+	synonymous_variant	Silent	SNP	G	G	A	rs150897748		TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93	20			ENST00000295589.3:c.1080C>T	p.Tyr360=	p.Y360=	ENST00000295589	NM_000730.2	360	taC/taT	0	0.627	AGGAGGAGGTGTAGGACAGGA
MUC7	4589	hgsc.bcm.edu;ucsc.edu	GRCh37	4	71347577	71347577	+	synonymous_variant	Silent	SNP	C	C	T	rs41424846	byFrequency	TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52	19			ENST00000413702.1:c.1116C>T	p.Asp372=	p.D372=	ENST00000413702	NM_001145006.1	372	gaC/gaT	0	0.338	GAATTATTGACGACATGGTGG
PPEF2	5470	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	76812812	76812812	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	224	99			ENST00000286719.7:c.230G>A	p.Ser77Asn	p.S77N	ENST00000286719	NM_006239.2	77	aGc/aAc	0	0.522	GTCGTTGTGGCTGCTGGGGAT
FAT4	79633	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	126239159	126239159	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	34	16			ENST00000394329.3:c.1593C>T	p.Leu531=	p.L531=	ENST00000394329	NM_024582.4	531	ctC/ctT	0	0.547	ATAGCGGCCTCGTGACCACTG
MARCH11	441061	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	16067657	16067657	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	124	45			ENST00000332432.8:c.1132A>G	p.Asn378Asp	p.N378D	ENST00000332432	NM_001102562.1	378	Aat/Gat	0	0.478	CTCATCCGATTGAACAGGTGC
PCDHA2	56146	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	140176070	140176070	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	43	13			ENST00000526136.1:c.1521C>T	p.Tyr507=	p.Y507=	ENST00000526136	NM_018905.2	507	taC/taT	0	0.682	TGTCGAGCTACGTTTCGGTGC
PCDHB2	56133	hgsc.bcm.edu;broad.mit.edu	GRCh37	5	140475880	140475880	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	116	15			ENST00000194155.4:c.1506C>T	p.Leu502=	p.L502=	ENST00000194155	NM_018936.2	502	ctC/ctT	0	0.692	ACCTGCCCCTCGCCTCCCTGG
PKHD1	5314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	51882309	51882309	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	110	26			ENST00000371117.3:c.5499G>A	p.Ser1833=	p.S1833=	ENST00000371117	NM_138694.3	1833	tcG/tcA	0	0.512	GGTAAGGCCACGATTCAAGCA
DDC	1644	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	50611629	50611629	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	166	38			ENST00000444124.2:c.155C>T	p.Thr52Met	p.T52M	ENST00000444124	NM_001082971.1	52	aCg/aTg	0	0.557	GTCCTCAAACGTGTCTGGCTC
GRM3	2913	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	86415593	86415593	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	257	69			ENST00000361669.2:c.485G>A	p.Arg162Gln	p.R162Q	ENST00000361669	NM_000840.2	162	cGg/cAg	0	0.522	AACCTGCTGCGGCTCTTCCAG
SLC26A3	1811	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	107423751	107423751	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79	21			ENST00000340010.5:c.1018G>A	p.Val340Ile	p.V340I	ENST00000340010	NM_000111.2	340	Gta/Ata	0	0.418	CAATCTCCTACGGTGTTTTGG
BRAF	673	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	90	22			ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	0	0.373	TAGACCAAAATCACCTATTTT
DAPK1	1612	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	90301560	90301560	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11	10			ENST00000408954.3:c.2319G>A	p.Met773Ile	p.M773I	ENST00000408954	NM_004938.2	773	atG/atA	0	0.577	CCAAAGGGATGCTGGAGGTGT
MUM1L1	139221	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	105449891	105449891	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6	14			ENST00000337685.2:c.466G>A	p.Ala156Thr	p.A156T	ENST00000337685	NM_152423.4	156	Gca/Aca	0	0.413	ATGCTTGTTAGCATCTTCAGA
HTR3C	170572	broad.mit.edu;ucsc.edu	GRCh37	3	183774718	183774718	+	stop_gained	Nonsense_Mutation	SNP	C	C	T			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	104	39			ENST00000318351.1:c.445C>T	p.Arg149Ter	p.R149*	ENST00000318351	NM_130770.2	149	Cga/Tga	0	0.478	CAGTGAAGGTCGAATTAAGTA
CLEC12A	160364	broad.mit.edu;ucsc.edu	GRCh37	12	10124176	10124176	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	32	19			ENST00000355690.4:c.11A>G	p.Asp4Gly	p.D4G	ENST00000355690	NM_001207010.1	4	gAt/gGt	0	0.318	CTTTGTCAAGATTTCTTTACA
UGT2B17	7367	broad.mit.edu;ucsc.edu	GRCh37	4	69434170	69434170	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	307	47			ENST00000317746.2:c.33G>A	p.Leu11=	p.L11=	ENST00000317746	NM_001077.3	11	ctG/ctA	0	0.423	TGAGCTGCATCAGCAGAAAGA
COBLL1	22837	broad.mit.edu;ucsc.edu	GRCh37	2	165578649	165578649	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58	21			ENST00000342193.4:c.932C>A	p.Ala311Glu	p.A311E	ENST00000342193	NM_014900.4	311	gCa/gAa	0	0.488	CTGGATGTGTGCAAGGTCTTG
RPSAP52	204010	broad.mit.edu;ucsc.edu	GRCh37	12	66152273	66152273	+	non_coding_transcript_exon_variant	RNA	SNP	T	T	G			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11	5			ENST00000489520.2:n.671A>C		*224*	ENST00000489520				0	0.498	TCTGACCCACTGAGGGAGCTC
RPL10L	140801	broad.mit.edu;ucsc.edu	GRCh37	14	47120403	47120403	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78	27			ENST00000298283.3:c.537C>T	p.Asp179=	p.D179=	ENST00000298283	NM_080746.2	179	gaC/gaT	0	0.517	CTTCAAATTCGTCAGCATTAA
ACSM2A	123876	broad.mit.edu;ucsc.edu	GRCh37	16	20476848	20476848	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs146541514		TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23	6			ENST00000573854.1:c.187C>T	p.Arg63Ter	p.R63*	ENST00000573854	NM_001010845.2	63	Cga/Tga	0	0.517	GGCTGGCAAGCGACTCCCAAG
SDK2	54549	broad.mit.edu;ucsc.edu	GRCh37	17	71410870	71410870	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26	16			ENST00000392650.3:c.2397C>T	p.His799=	p.H799=	ENST00000392650	NM_001144952.1	799	caC/caT	0	0.597	TGGCTTCCGCGTGCACATTGC
NF1	4763	broad.mit.edu;hgsc.bcm.edu	GRCh37	17	29548901	29548901	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-			TCGA-DU-6402-01	TCGA-DU-6402-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	44	23			ENST00000358273.4:c.1675delG	p.Asp559IlefsTer9	p.D559Ifs*9	ENST00000358273	NM_001042492.2	559	Gat/at	0	0.289	AGATAGCATTGATTTGTGGAA
NUP98	4928	hgsc.bcm.edu;broad.mit.edu	GRCh37	11	3697451	3697451	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-P5-A5EX-01	TCGA-P5-A5EX-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	129	11			ENST00000324932.7:c.5341A>G	p.Met1781Val	p.M1781V	ENST00000324932	NM_139132.3	1781	Atg/Gtg	0	0.582	AGTTCGTCCATGGCATAGTCC
FBXL3	26224	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	13	77581815	77581815	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-P5-A5EX-01	TCGA-P5-A5EX-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	49	23			ENST00000355619.5:c.752G>A	p.Arg251Gln	p.R251Q	ENST00000355619	NM_012158.2	251	cGa/cAa	0	0.418	ATGTTCTAATCGAACATGTTT
KIAA1024	23251	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	79749239	79749239	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-P5-A5EX-01	TCGA-P5-A5EX-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84	27			ENST00000305428.3:c.750C>T	p.Val250=	p.V250=	ENST00000305428	NM_015206.2	250	gtC/gtT	0	0.473	CATTTGTGGTCCAGTCCTGTG
BZRAP1	9256	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	56388978	56388978	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-P5-A5EX-01	TCGA-P5-A5EX-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97	41			ENST00000343736.4:c.3035A>G	p.Asn1012Ser	p.N1012S	ENST00000343736		1012	aAc/aGc	0	0.602	CCGGACACCGTTGGATGTGCC
PRX	57716	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	40901791	40901791	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-P5-A5EX-01	TCGA-P5-A5EX-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	115	11			ENST00000324001.7:c.2468C>T	p.Ala823Val	p.A823V	ENST00000324001	NM_181882.2	823	gCg/gTg	0	0.587	CTCAGCACCCGCCTCGCCTGG
SOGA1	140710	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	20	35445831	35445831	+	synonymous_variant	Silent	SNP	G	G	T			TCGA-P5-A5EX-01	TCGA-P5-A5EX-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6	8			ENST00000237536.4:c.1113C>A	p.Ala371=	p.A371=	ENST00000237536	NM_080627.2	371	gcC/gcA	0	0.458	TCTTCTTATCGGCCTTCCCCA
ZC3H6	376940	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	113089666	113089666	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-P5-A5EX-01	TCGA-P5-A5EX-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	25	16			ENST00000409871.1:c.3171A>G	p.Ser1057=	p.S1057=	ENST00000409871	NM_198581.2	1057	tcA/tcG	0	0.443	ACGGTTCATCATCCACATCAG
TTN	7273	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	179410161	179410161	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-P5-A5EX-01	TCGA-P5-A5EX-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	92	51			ENST00000589042.1:c.95676T>C	p.Ser31892=	p.S31892=	ENST00000589042	NM_001267550.1	31892	agT/agC	0	0.468	CGCTGGGCTCACTGTTACCAG
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-P5-A5EX-01	TCGA-P5-A5EX-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	59	17			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
BOD1L1	259282	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	13603085	13603085	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-P5-A5EX-01	TCGA-P5-A5EX-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	189	24			ENST00000040738.5:c.5439C>T	p.Ser1813=	p.S1813=	ENST00000040738	NM_148894.2	1813	agC/agT	0	0.488	CAAAGCCTTCGCTGCTATCTT
NMBR	4829	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	142397180	142397180	+	missense_variant	Missense_Mutation	SNP	T	T	A			TCGA-P5-A5EX-01	TCGA-P5-A5EX-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	59	25			ENST00000258042.1:c.778A>T	p.Thr260Ser	p.T260S	ENST00000258042	NM_002511.2	260	Aca/Tca	0	0.388	CGTTTCCGTGTTTCCATCTGC
WIPI2	26100	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	5256804	5256804	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-P5-A5EX-01	TCGA-P5-A5EX-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45	20			ENST00000288828.4:c.562G>A	p.Asp188Asn	p.D188N	ENST00000288828	NM_001278299.1	188	Gat/Aat	0	0.527	GCAGGTCTTCGATACCATTAA
COA1	55744	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	43687182	43687182	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-P5-A5EX-01	TCGA-P5-A5EX-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79	37			ENST00000395879.1:c.67G>A	p.Gly23Ser	p.G23S	ENST00000395879		23	Ggt/Agt	0	0.493	TAGAACACACCGTGGAAAAGG
CROT	54677	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	87005181	87005181	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-P5-A5EX-01	TCGA-P5-A5EX-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40	11			ENST00000419147.2:c.872T>C	p.Leu291Ser	p.L291S	ENST00000419147	NM_001143935.1	291	tTg/tCg	0	0.368	CCAGAGAACTTGGCTTTGTTA
FOXP2	93986	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	114294061	114294061	+	missense_variant	Missense_Mutation	SNP	A	A	T			TCGA-P5-A5EX-01	TCGA-P5-A5EX-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	85	31			ENST00000408937.3:c.1338A>T	p.Lys446Asn	p.K446N	ENST00000408937	NM_014491.3	446	aaA/aaT	0	0.393	CATCTCCCAAACCtgtaagtg
KEL	3792	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	142638440	142638440	+	stop_gained	Nonsense_Mutation	SNP	G	G	A			TCGA-P5-A5EX-01	TCGA-P5-A5EX-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	145	60			ENST00000355265.2:c.2098C>T	p.Arg700Ter	p.R700*	ENST00000355265	NM_000420.2	700	Cga/Tga	0	0.622	CCGTGGACTCGGAGGTGTGGA
BARX1	56033	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	96714489	96714489	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-P5-A5EX-01	TCGA-P5-A5EX-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	34	19			ENST00000253968.6:c.722C>T	p.Ala241Val	p.A241V	ENST00000253968	NM_021570.3	241	gCg/gTg	0	0.682	CGGCACCTCCGCCGGTTTCTC
MAGEB1	4112	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	30269583	30269583	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-P5-A5EX-01	TCGA-P5-A5EX-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93	43			ENST00000378981.3:c.973C>T	p.Arg325Cys	p.R325C	ENST00000378981	NM_002363.4	325	Cgt/Tgt	0	0.527	TAGAGCCAGGCGTCGCACTAC
KIF4A	24137	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	69615591	69615591	+	missense_variant	Missense_Mutation	SNP	T	T	G			TCGA-P5-A5EX-01	TCGA-P5-A5EX-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57	41			ENST00000374403.3:c.2303T>G	p.Leu768Arg	p.L768R	ENST00000374403	NM_012310.4	768	cTt/cGt	0	0.438	AATGACCTCCTTGAAGATAGA
BRWD3	254065	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	79942476	79942476	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-P5-A5EX-01	TCGA-P5-A5EX-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	43	14			ENST00000373275.4:c.3891T>C	p.Ser1297=	p.S1297=	ENST00000373275	NM_153252.4	1297	tcT/tcC	0	0.383	TACACTTTAAAGACTGTCTTC
TENM1	10178	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	123519691	123519691	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-P5-A5EX-01	TCGA-P5-A5EX-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	119	63			ENST00000422452.2:c.5912C>G	p.Thr1971Arg	p.T1971R	ENST00000422452	NM_001163279.1	1971	aCa/aGa	0	0.483	TCTGCGCCCTGTCCCCAGATG
ZNF551	90233	broad.mit.edu;ucsc.edu	GRCh37	19	58197953	58197953	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-P5-A5EX-01	TCGA-P5-A5EX-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	53	64			ENST00000282296.5:c.310A>G	p.Ser104Gly	p.S104G	ENST00000282296		104	Agt/Ggt	0	0.478	AACTCACCTCAGTGAGATTAA
CLDN11	5010	broad.mit.edu;ucsc.edu	GRCh37	3	170141061	170141061	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-P5-A5EX-01	TCGA-P5-A5EX-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	116	54			ENST00000064724.3:c.337G>A	p.Gly113Ser	p.G113S	ENST00000064724	NM_005602.5	113	Ggt/Agt	0	0.602	CCAGGAGCCCGGTGTGGCTAA
KIAA1429	25962	broad.mit.edu;hgsc.bcm.edu	GRCh37	8	95541443	95541445	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-			TCGA-P5-A5EX-01	TCGA-P5-A5EX-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28	10			ENST00000297591.5:c.733_735delCAA	p.Gln245del	p.Q245del	ENST00000297591	NM_015496.4	245	CAA/-	0	0.438	ctccttcttcttgttgttcctct
MPRIP	23164	broad.mit.edu;hgsc.bcm.edu	GRCh37	17	17046885	17046886	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C			TCGA-P5-A5EX-01	TCGA-P5-A5EX-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	51	18			ENST00000395811.5:c.1058dupC	p.Ala354SerfsTer43	p.A354Sfs*43	ENST00000395811	NM_015134.3	351	gcc/gCcc	0	0.649	CACCAATGAAGCCCCCCCAGCT
AKR1C3	8644	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	5144389	5144389	+	stop_gained	Nonsense_Mutation	SNP	C	C	T			TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61	18			ENST00000380554.3:c.667C>T	p.Arg223Ter	p.R223*	ENST00000380554	NM_003739.5	223	Cga/Tga	0	0.383	GGGATCTCAACGAGACAAACG
KIAA1217	56243	hgsc.bcm.edu;broad.mit.edu	GRCh37	10	24825812	24825812	+	missense_variant	Missense_Mutation	SNP	A	A	T			TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	65	6			ENST00000376454.3:c.3524A>T	p.Lys1175Met	p.K1175M	ENST00000376454	NM_019590.3	1175	aAg/aTg	0	0.507	GTGCCACCCAAGGAGAAGAAG
LRP1	4035	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	57588464	57588464	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	48	13			ENST00000243077.3:c.8173G>A	p.Glu2725Lys	p.E2725K	ENST00000243077	NM_002332.2	2725	Gag/Aag	0	0.597	TGAACATGGCGAGGACGAGAC
KLC1	3831	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	14	104143843	104143843	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	48	23			ENST00000452929.2:c.1471A>G	p.Met491Val	p.M491V	ENST00000452929	NM_001130107.1	491	Atg/Gtg	0	0.398	AGAAGCTGCTATGAGGTCTCG
MYO5A	4644	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	52720613	52720613	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	92	42			ENST00000399231.3:c.292C>G	p.Leu98Val	p.L98V	ENST00000399231	NM_000259.3	98	Ctt/Gtt	0	0.408	GTATAAATAAGTTTGGAATCA
CLCN7	1186	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	1510460	1510460	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64	32			ENST00000382745.4:c.553G>A	p.Ala185Thr	p.A185T	ENST00000382745	NM_001287.5	185	Gcc/Acc	0	0.597	AGCACGAAGGCGGCGTTCAGC
CDH15	1013	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	89261356	89261356	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	16	9			ENST00000289746.2:c.2238G>A	p.Ala746=	p.A746=	ENST00000289746	NM_004933.2	746	gcG/gcA	0	0.632	GCTCGGTGGCGGGGACGCTGA
CCR10	2826	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	40832563	40832563	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29	8			ENST00000332438.4:c.97A>G	p.Lys33Glu	p.K33E	ENST00000332438	NM_016602.2	33	Aag/Gag	0	0.637	ACATCGGCCTTGTAGCAAAGC
BRINP2	57795	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	177247827	177247827	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	103	48			ENST00000361539.4:c.1141G>A	p.Val381Met	p.V381M	ENST00000361539	NM_021165.2	381	Gtg/Atg	0	0.607	TGGCTTGAAAGTGCTGTTCAA
SIPA1L2	57568	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	232607260	232607260	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75	26			ENST00000366630.1:c.2100G>A	p.Arg700=	p.R700=	ENST00000366630		700	agG/agA	0	0.383	TTCCTATGTGCCTTTTCCTCA
NCAPH2	29781	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	22	50956005	50956005	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A			TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	72	30			ENST00000299821.11:c.267-1G>A		p.X89_splice	ENST00000299821				0	0.632	TTCTCTCTCAGGCGGGCCAAG
ALMS1	7840	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	73836722	73836722	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	81	14			ENST00000264448.6:c.12487A>G	p.Lys4163Glu	p.K4163E	ENST00000264448	NM_015120.4	4163	Aaa/Gaa	0	0.433	TCTGGGGAGAAAAGTTCCCTG
MARCO	8685	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	119739756	119739756	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	27	16			ENST00000327097.4:c.926C>T	p.Pro309Leu	p.P309L	ENST00000327097	NM_006770.3	309	cCg/cTg	0	0.642	CAGGGTGTTCCGGGCCCTCCT
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	72	17			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
BBS7	55212	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	122782768	122782768	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11	25			ENST00000264499.4:c.232C>T	p.Pro78Ser	p.P78S	ENST00000264499	NM_176824.2	78	Cct/Tct	0	0.418	TTCTCCTGAGGTGTGTTGATA
CAST	831	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	96077000	96077000	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33	22			ENST00000395812.2:c.826G>A	p.Ala276Thr	p.A276T	ENST00000395812	NM_001042440.2	276	Gcc/Acc	0	0.433	TGCTATAGACGCCTTGTCATC
FUCA2	2519	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	143823182	143823182	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	32	24			ENST00000002165.6:c.1041A>G	p.Val347=	p.V347=	ENST00000002165	NM_032020.4	347	gtA/gtG	0	0.408	CCTCAAAAACTACAGAAATGG
NRCAM	4897	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	107808830	107808830	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	32	6			ENST00000379028.3:c.3205A>G	p.Arg1069Gly	p.R1069G	ENST00000379028		1069	Agg/Ggg	0	0.353	TTGCTGATCCTGGGATTTACT
RAB2A	5862	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	61484623	61484623	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36	11			ENST00000262646.7:c.137G>A	p.Arg46Gln	p.R46Q	ENST00000262646	NM_002865.2	46	cGa/cAa	0	0.323	TTCGGTGCTCGAATGATAACT
SPANXD	64648	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	140785767	140785767	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	53	78			ENST00000370515.3:c.149T>C	p.Ile50Thr	p.I50T	ENST00000370515	NM_145665.1	50	aTa/aCa	0	0.498	AACCACTAGTATGGTCGAGGA
OR1A1	8383	broad.mit.edu;ucsc.edu	GRCh37	17	3119138	3119138	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	134	50			ENST00000304094.1:c.224C>T	p.Ser75Leu	p.S75L	ENST00000304094	NM_014565.2	75	tCg/tTg	0	0.483	TTCTTCTCATCGGTAACCATC
HIST1H3C	8352	broad.mit.edu;ucsc.edu	GRCh37	6	26045799	26045799	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35	5			ENST00000540144.1:c.161G>A	p.Arg54His	p.R54H	ENST00000540144	NM_003531.2	54	cGc/cAc	0	0.622	GAAATCCGTCGCTACCAGAAG
OBSCN	84033	broad.mit.edu;ucsc.edu	GRCh37	1	228529314	228529314	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A			TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	20	5			ENST00000570156.2:c.20904G>A	p.Trp6968Ter	p.W6968*	ENST00000570156	NM_001271223.2	6968	tgG/tgA	0	0.672	TGCCTGTGTGGCGTGAGTGTC
HCLS1	3059	broad.mit.edu;ucsc.edu	GRCh37	3	121351926	121351926	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21	6			ENST00000314583.3:c.996G>T	p.Gln332His	p.Q332H	ENST00000314583	NM_005335.4	332	caG/caT	0	0.587	CCGGGAGAGTCTGCCTAATGG
CLK1	1195	broad.mit.edu;hgsc.bcm.edu	GRCh37	2	201726490	201726493	+	frameshift_variant	Frame_Shift_Del	DEL	CTTC	CTTC	-			TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	165	45			ENST00000434813.2:c.219_222delGAAG	p.Lys74AspfsTer30	p.K74Dfs*30	ENST00000434813	NM_001162407.1	73	agGAAG/ag	0	0.397	TATGTGATCTCTTCCTTCTTTTAT
RBPJ	3516	broad.mit.edu;hgsc.bcm.edu	GRCh37	4	26426086	26426088	+	inframe_deletion	In_Frame_Del	DEL	TTT	TTT	-			TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78	28			ENST00000342295.1:c.661_663delTTT	p.Phe221del	p.F221del	ENST00000342295	NM_005349.3	220	TTT/-	0	0.36	GTGGGGAGCCTTTTTTATTCATC
ZFHX4	79776	broad.mit.edu;hgsc.bcm.edu	GRCh37	8	77776374	77776377	+	frameshift_variant	Frame_Shift_Del	DEL	CAAT	CAAT	-	rs76951673		TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	44	22			ENST00000521891.2:c.10427_10430delTCAA	p.Ile3476AsnfsTer4	p.I3476Nfs*4	ENST00000521891	NM_024721.4	3475	aCAATc/ac	0	0.456	AAAGAGAAAACAATCAAACAAGCA
RBM12B	389677	broad.mit.edu;hgsc.bcm.edu	GRCh37	8	94745644	94745648	+	frameshift_variant	Frame_Shift_Del	DEL	TTAAC	TTAAC	-			TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47	19			ENST00000399300.2:c.2991_2995delGTTAA	p.Lys997AsnfsTer10	p.K997Nfs*10	ENST00000399300	NM_203390.2	997	aaGTTAAct/aact	0	0.332	TACAGCAAAGTTAACTTAACTTTTC
C12orf65	91574	broad.mit.edu;hgsc.bcm.edu	GRCh37	12	123738357	123738359	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-			TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	51	10			ENST00000253233.1:c.139_141delAAG	p.Lys47del	p.K47del	ENST00000253233	NM_152269.4	46	AAG/-	0	0.557	GATGGCAGGCAAGAAGGACTACC
UBL3	5412	broad.mit.edu;hgsc.bcm.edu	GRCh37	13	30341404	30341406	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-			TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	38	12			ENST00000380680.4:c.340_342delTGT	p.Cys114del	p.C114del	ENST00000380680	NM_007106.3	114	TGT/-	0	0.433	ACAGGATTACACAACAATTACTC
TINF2	26277	broad.mit.edu;hgsc.bcm.edu	GRCh37	14	24709491	24709493	+	inframe_deletion	In_Frame_Del	DEL	TAA	TAA	-			TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	80	19			ENST00000267415.7:c.1105_1107delTTA	p.Leu369del	p.L369del	ENST00000267415	NM_001099274.1	369	TTA/-	0	0.498	CCCTAGGAGGTAATAATGATAGT
PAF1	54623	broad.mit.edu;hgsc.bcm.edu	GRCh37	19	39879756	39879758	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-			TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	104	30			ENST00000221265.3:c.542_544delAGA	p.Lys181del	p.K181del	ENST00000221265	NM_019088.3	181	aAGAct/act	0	0.483	TCCTCAAAAGTCTTCTCAATGGC
CIC	23152	broad.mit.edu;hgsc.bcm.edu	GRCh37	19	42797980	42797981	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-			TCGA-FG-5964-01	TCGA-FG-5964-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	35	32			ENST00000575354.2:c.4034_4035delTG	p.Val1345GlyfsTer16	p.V1345Gfs*16	ENST00000575354	NM_015125.3	1344	tcTGtg/tctg	0	0.693	CCTTTGACTCTGTGGACAAGTG
YME1L1	10730	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	27420861	27420861	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DH-A66F-01	TCGA-DH-A66F-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47	20			ENST00000326799.3:c.956G>A	p.Arg319Gln	p.R319Q	ENST00000326799	NM_139312.2	319	cGg/cAg	0	0.373	TGTTGTTGTCCGGAAGCGGAC
HPS5	11234	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	18339305	18339305	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DH-A66F-01	TCGA-DH-A66F-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	12	8			ENST00000349215.3:c.101G>A	p.Arg34His	p.R34H	ENST00000349215	NM_181507.1	34	cGt/cAt	0	0.463	CACCTTTAGACGACTGGAGTC
PLEKHG6	55200	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	6422805	6422805	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DH-A66F-01	TCGA-DH-A66F-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91	44			ENST00000396988.3:c.149G>A	p.Arg50His	p.R50H	ENST00000396988	NM_001144856.1	50	cGc/cAc	0	0.637	GATCCCAGTCGCCGACGCCTC
SLC6A2	6530	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	55735794	55735794	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DH-A66F-01	TCGA-DH-A66F-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	101	40			ENST00000219833.8:c.1778C>T	p.Thr593Met	p.T593M	ENST00000219833	NM_001172504.1	593	aCg/aTg	0	0.622	TATGGCATCACGCCAGAGAAC
TRPV2	51393	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	16321163	16321163	+	stop_gained	Nonsense_Mutation	SNP	C	C	T			TCGA-DH-A66F-01	TCGA-DH-A66F-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45	14			ENST00000338560.7:c.181C>T	p.Arg61Ter	p.R61*	ENST00000338560	NM_016113.4	61	Cga/Tga	0	0.597	CCTCAACTACCGAAAGGGAAC
UNC13D	201294	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	73832286	73832286	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DH-A66F-01	TCGA-DH-A66F-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29	5			ENST00000207549.4:c.1441G>A	p.Val481Met	p.V481M	ENST00000207549	NM_199242.2	481	Gtg/Atg	0	0.667	CTCACCTGCACCATGGGTTGA
UNC13A	23025	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	17752214	17752214	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-DH-A66F-01	TCGA-DH-A66F-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45	24			ENST00000519716.2:c.2624A>G	p.Tyr875Cys	p.Y875C	ENST00000519716	NM_001080421.2	875	tAc/tGc	0	0.592	CATGGCTTGGTAGATGGACTC
KIR2DL1	3802	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	55285048	55285048	+	missense_variant	Missense_Mutation	SNP	T	T	A			TCGA-DH-A66F-01	TCGA-DH-A66F-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	126	95			ENST00000336077.6:c.334T>A	p.Ser112Thr	p.S112T	ENST00000336077	NM_014218.2	112	Tca/Aca	0	0.522	CTATCAGGTGTCAGCTCCCAG
FOXS1	2307	hgsc.bcm.edu;broad.mit.edu	GRCh37	20	30432674	30432674	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DH-A66F-01	TCGA-DH-A66F-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91	6			ENST00000375978.3:c.672C>T	p.Phe224=	p.F224=	ENST00000375978	NM_004118.3	224	ttC/ttT	0	0.587	CAGCCTCTGAGAAGCCGGCAG
ZNF335	63925	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	20	44578967	44578967	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-DH-A66F-01	TCGA-DH-A66F-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82	55			ENST00000322927.2:c.3378C>G	p.His1126Gln	p.H1126Q	ENST00000322927	NM_022095.3	1126	caC/caG	0	0.582	CATCAGGACTGTGCAGCCGCT
SYNJ1	8867	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	21	34038343	34038343	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DH-A66F-01	TCGA-DH-A66F-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	22	11			ENST00000433931.2:c.2172C>T	p.Phe724=	p.F724=	ENST00000433931	NM_003895.3	724	ttC/ttT	0	0.423	GGCTACAGACGAAGCAAAGGC
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-DH-A66F-01	TCGA-DH-A66F-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	34	22			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
ITIH3	3699	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	52840399	52840399	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DH-A66F-01	TCGA-DH-A66F-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	44	13			ENST00000449956.2:c.2033G>A	p.Arg678His	p.R678H	ENST00000449956	NM_002217.3	678	cGc/cAc	0	0.612	ACAGTGCTGCGCCTTATTCAG
SLC23A1	9963	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	138713162	138713162	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-DH-A66F-01	TCGA-DH-A66F-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28	23			ENST00000353963.3:c.1490T>C	p.Leu497Pro	p.L497P	ENST00000353963	NM_152685.3	497	cTg/cCg	0	0.527	CAGCACAATCAGAATCTGATC
ARID1B	57492	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	157495231	157495231	+	stop_gained	Nonsense_Mutation	SNP	C	C	T			TCGA-DH-A66F-01	TCGA-DH-A66F-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64	9			ENST00000346085.5:c.3115C>T	p.Gln1039Ter	p.Q1039*	ENST00000346085	NM_020732.3	1039	Cag/Tag	0	0.522	AGGCACTCCACAGCCCGAGAG
COL15A1	1306	broad.mit.edu;ucsc.edu	GRCh37	9	101832036	101832036	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DH-A66F-01	TCGA-DH-A66F-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	123	68			ENST00000375001.3:c.4035G>A	p.Ala1345=	p.A1345=	ENST00000375001	NM_001855.4	1345	gcG/gcA	0	0.537	GGCGAACCGCGGACACAGCGG
ASCC1	51008	broad.mit.edu;hgsc.bcm.edu	GRCh37	10	73970535	73970535	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-			TCGA-DH-A66F-01	TCGA-DH-A66F-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45	18			ENST00000342444.4:c.167delC	p.Pro56HisfsTer8	p.P56Hfs*8	ENST00000342444	NM_001198799.2	56	cCa/ca	0	0.527	GAATCCTTGTGGGGTCTGCTC
CIC	23152	broad.mit.edu	GRCh37	19	42792001	42792001	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-DH-A66F-01	TCGA-DH-A66F-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	4	6			ENST00000575354.2:c.805T>C	p.Trp269Arg	p.W269R	ENST00000575354	NM_015125.3	269	Tgg/Cgg	0	0.632	AGATTGGAAGTGGTGCAACAA
SERPING1	710	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	57367766	57367766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139035354	by1000genomes	TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	72	57			ENST00000278407.4:c.466G>A	p.Ala156Thr	p.A156T	ENST00000278407	NM_000062.2	156	Gcc/Acc	0	0.542	GCTCTACCACGCCTTCTCAGC
MS4A14	84689	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	60183353	60183353	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	31	27			ENST00000531783.1:c.1011T>C	p.Phe337=	p.F337=	ENST00000531783	NM_001261828.1	337	ttT/ttC	0	0.423	TCCAAGTTTTTCCATCCCATT
TMTC1	83857	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	29659825	29659825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35279918		TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78	33			ENST00000539277.1:c.2603G>A	p.Arg868His	p.R868H	ENST00000539277	NM_001193451.1	868	cGc/cAc	0	0.453	TTTTTCTAGGCGATCCAATTT
DCLK1	9201	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	13	36686247	36686247	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	43	13			ENST00000255448.4:c.482G>A	p.Arg161Gln	p.R161Q	ENST00000255448	NM_004734.4	161	cGg/cAg	0	0.522	AGACACTGCCCGAGAAGCCGA
DIS3	22894	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	13	73346337	73346337	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28	17			ENST00000377767.4:c.1463A>G	p.Asp488Gly	p.D488G	ENST00000377767	NM_014953.3	488	gAt/gGt	0	0.363	ATGTAGAGCATCGTCTATATC
FOXG1	2290	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	14	29237034	29237034	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	22	12			ENST00000382535.3:c.549G>A	p.Pro183=	p.P183=	ENST00000382535		183	ccG/ccA	0	0.637	AGAAGCCGCCGTTCAGCTACA
ISM2	145501	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	14	77942239	77942239	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	25	8			ENST00000342219.4:c.1415C>T	p.Ala472Val	p.A472V	ENST00000342219	NM_199296.2	472	gCg/gTg	0	0.677	GCAGAAGCGCGCCGTGGGCTG
TTYH2	94015	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	72249349	72249349	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	66	20			ENST00000269346.4:c.1389G>A	p.Gln463=	p.Q463=	ENST00000269346	NM_032646.5	463	caG/caA	0	0.647	TGGGAAGTCAGACCAGCCTGC
EVPL	2125	hgsc.bcm.edu;broad.mit.edu	GRCh37	17	74003681	74003681	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	55	5			ENST00000301607.3:c.5605G>A	p.Val1869Met	p.V1869M	ENST00000301607	NM_001988.2	1869	Gtg/Atg	0	0.617	AGCAGGTCCACGATGCCCCCT
C3	718	hgsc.bcm.edu;broad.mit.edu	GRCh37	19	6712560	6712560	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	206	15			ENST00000245907.6:c.1078A>G	p.Thr360Ala	p.T360A	ENST00000245907	NM_000064.2	360	Aca/Gca	0	0.622	TACTTGGGTGTCTTGGTGAAG
ALG6	29929	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	63876858	63876858	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	152	56			ENST00000371108.4:c.536T>C	p.Leu179Pro	p.L179P	ENST00000371108	NM_013339.3	179	cTt/cCt	0	0.363	TGGGGTGTTCTTGGAATATCT
DLGAP4	22839	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	20	35060961	35060961	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8	11			ENST00000373913.3:c.841G>T	p.Gly281Trp	p.G281W	ENST00000373913		281	Ggg/Tgg	0	0.632	CCCCAGCCTTGGGGTGGGCAC
LRP2	4036	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	170038748	170038748	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95	34			ENST00000263816.3:c.9927G>A	p.Gln3309=	p.Q3309=	ENST00000263816	NM_004525.2	3309	caG/caA	0	0.532	CCACACAGTGCTGGGCCAGCA
ANKAR	150709	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	190585366	190585366	+	missense_variant	Missense_Mutation	SNP	A	A	C			TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	49	20			ENST00000520309.1:c.2488A>C	p.Asn830His	p.N830H	ENST00000520309	NM_144708.3	830	Aat/Cat	0	0.284	AAGCCTGATAAATCTATTGAA
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	50	38			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
SETD2	29072	hgsc.bcm.edu;broad.mit.edu	GRCh37	3	47103767	47103767	+	stop_gained	Nonsense_Mutation	SNP	G	G	C			TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	156	8			ENST00000409792.3:c.6179C>G	p.Ser2060Ter	p.S2060*	ENST00000409792	NM_014159.6	2060	tCa/tGa	0	0.463	TCTCTCTCTTGACCTATTAGG
CCDC54	84692	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	107097101	107097101	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42	27			ENST00000261058.1:c.667C>T	p.Arg223Cys	p.R223C	ENST00000261058	NM_032600.2	223	Cgt/Tgt	0	0.378	TCTGAAGAAACGTAACCATCA
SLC9C1	285335	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	111887770	111887770	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58	20			ENST00000305815.5:c.3191G>A	p.Arg1064Gln	p.R1064Q	ENST00000305815	NM_183061.1	1064	cGa/cAa	0	0.323	ATAAGTTTTTCGTAACAGACA
TRPC7	57113	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	135561020	135561020	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	16	9			ENST00000513104.1:c.2285T>C	p.Met762Thr	p.M762T	ENST00000513104	NM_020389.2	762	aTg/aCg	0	0.453	AGAATTCCTCATGCCAGCCTG
LY6G6D	58530	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	31685399	31685399	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	199	97			ENST00000375825.3:c.220G>A	p.Ala74Thr	p.A74T	ENST00000375825	NM_021246.2	74	Gcc/Acc	0	0.577	CTGCGTCGCAGCCCATCATTG
DST	667	hgsc.bcm.edu;ucsc.edu	GRCh37	6	56483529	56483529	+	intron_variant	Intron	SNP	G	G	A			TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64	21			ENST00000244364.6:c.3319-4247C>T		*1107*	ENST00000244364	NM_015548.4			0	0.358	ATCATTTTCAGTGATGACTTT
EEF1A1	1915	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	74229668	74229668	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	43	15			ENST00000316292.9:c.82A>G	p.Ile28Val	p.I28V	ENST00000316292	NM_001402.5	28	Atc/Gtc	0	0.413	CATTTATAGATCAGATGGCCA
CD36	948	hgsc.bcm.edu;broad.mit.edu	GRCh37	7	80286000	80286000	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	83	4			ENST00000435819.1:c.265G>A	p.Gly89Ser	p.G89S	ENST00000435819		89	Ggt/Agt	0	0.398	TAAGCAAAGAGGTCCTTATAC
TBC1D2	55357	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	100991314	100991314	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	43	13			ENST00000375066.5:c.898C>T	p.Arg300Trp	p.R300W	ENST00000375066	NM_018421.3	300	Cgg/Tgg	0	0.522	GTTCGGTTCCGTGTGATTCCT
OR13D1	286365	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	107456818	107456818	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	27	7			ENST00000318763.5:c.116C>G	p.Ser39Cys	p.S39C	ENST00000318763	NM_001004484.1	39	tCt/tGt	0	0.423	AGAAATTACTCTGCCATGACT
MUSK	4593	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	113562782	113562782	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	121	32			ENST00000374448.4:c.2124G>C	p.Gln708His	p.Q708H	ENST00000374448	NM_005592.3	708	caG/caC	0	0.567	TTGCCAGGCAGGTGGCAGCTG
PTGS1	5742	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	125154668	125154668	+	missense_variant	Missense_Mutation	SNP	T	T	G			TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67	26			ENST00000362012.2:c.1645T>G	p.Phe549Val	p.F549V	ENST00000362012	NM_000962.3	549	Ttt/Gtt	0	0.537	GCCGAGCACATTTGGCGGCGA
HCCS	3052	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	11135492	11135492	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	34	43			ENST00000321143.4:c.358T>C	p.Tyr120His	p.Y120H	ENST00000321143	NM_005333.4	120	Tac/Cac	0	0.383	AAAGTGGGTTTACCCTTCTGA
NOL8	55035	broad.mit.edu;ucsc.edu	GRCh37	9	95077012	95077012	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11	6			ENST00000545558.1:c.1895A>G	p.His632Arg	p.H632R	ENST00000545558		632	cAt/cGt	0	0.453	CTTCTTTGCATGTTGGCATGG
EFTUD2	9343	broad.mit.edu;ucsc.edu	GRCh37	17	42931994	42931994	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	31	18			ENST00000426333.2:c.2189G>A	p.Arg730His	p.R730H	ENST00000426333	NM_001142605.1	730	cGt/cAt	0	0.567	CCAGATGGAACGGGCAGCCAG
SSPO	23145	broad.mit.edu;ucsc.edu	GRCh37	7	149482723	149482723	+	non_coding_transcript_exon_variant	RNA	SNP	C	C	G			TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7	5			ENST00000378016.2:n.3139C>G		*1047*	ENST00000378016				0	0.627	GGCCAGTGGCCTATTCACAGT
IQGAP1	8826	broad.mit.edu;ucsc.edu	GRCh37	15	91034589	91034589	+	stop_gained	Nonsense_Mutation	SNP	C	C	T			TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	27	4			ENST00000268182.5:c.4273C>T	p.Gln1425Ter	p.Q1425*	ENST00000268182	NM_003870.3	1425	Cag/Tag	0	0.398	GAGAGCCATGCAGAGACGTGC
SYNE2	23224	broad.mit.edu;ucsc.edu	GRCh37	14	64676802	64676802	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	19	8			ENST00000358025.3:c.18683A>G	p.Asn6228Ser	p.N6228S	ENST00000358025	NM_182914.2	6228	aAc/aGc	0	0.622	CGCTGGGACAACCTTCAGAGG
KLHL28	54813	broad.mit.edu;hgsc.bcm.edu	GRCh37	14	45415078	45415078	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-			TCGA-HT-7684-01	TCGA-HT-7684-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	59	21			ENST00000396128.4:c.54delT	p.Glu19AsnfsTer7	p.E19Nfs*7	ENST00000396128	NM_017658.3	18	tcT/tc	0	0.403	GAAGTTGTTCAGAATGCAAGT
TLL2	7093	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	98129891	98129891	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84	11			ENST00000357947.3:c.2844C>T	p.Tyr948=	p.Y948=	ENST00000357947	NM_012465.3	948	taC/taT	0	0.667	CCATGTAGTCGTAGCCGCAGT
OR5I1	10798	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	55703053	55703053	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29	16			ENST00000301532.3:c.824T>C	p.Ile275Thr	p.I275T	ENST00000301532	NM_006637.1	275	aTt/aCt	0	0.408	CACTGAGATAATTTTATCAGT
LRRC55	219527	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	56949447	56949447	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64	11			ENST00000497933.1:c.80A>G	p.Asp27Gly	p.D27G	ENST00000497933	NM_001005210.2	27	gAc/gGc	0	0.607	GATTCCATGGACACAGTCCTC
CASP1	834	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	104897057	104897057	+	missense_variant	Missense_Mutation	SNP	A	A	C			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84	8			ENST00000533400.1:c.1143T>G	p.Asp381Glu	p.D381E	ENST00000533400	NM_001257118.1	381	gaT/gaG	0	0.393	GCGCTCTACCATCTGGCTGCT
CLEC12A	160364	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	10131591	10131591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141455664	byFrequency	TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73	46			ENST00000355690.4:c.148C>T	p.Arg50Cys	p.R50C	ENST00000355690	NM_001207010.1	50	Cgt/Tgt	0	0.433	TCATGTATGGCGTCCAGCAGC
SRRM4	84530	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	119592158	119592158	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	19	18			ENST00000267260.4:c.1502C>T	p.Pro501Leu	p.P501L	ENST00000267260	NM_194286.3	501	cCg/cTg	0	0.632	AGAGACTCCCCGAGCCACCTG
NEMF	9147	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	14	50269393	50269393	+	synonymous_variant	Silent	SNP	A	A	C			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	55	6			ENST00000298310.5:c.1968T>G	p.Leu656=	p.L656=	ENST00000298310		656	ctT/ctG	0	0.318	GTACCTTAAAAAGGAAGCTAA
SYNE2	23224	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	14	64683079	64683079	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	51	38			ENST00000358025.3:c.19516T>C	p.Ser6506Pro	p.S6506P	ENST00000358025	NM_182914.2	6506	Tcc/Ccc	0	0.498	TCCCCCTGCGTCCAGCACCCC
CHRNA5	1138	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	78882881	78882881	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	59	34			ENST00000299565.5:c.1148G>A	p.Gly383Asp	p.G383D	ENST00000299565	NM_000745.3	383	gGt/gAt	0	0.438	ACTGAGAGTGGTAGTGGACCA
ABR	29	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	915191	915191	+	stop_gained	Nonsense_Mutation	SNP	G	G	A			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78	55			ENST00000302538.5:c.1996C>T	p.Gln666Ter	p.Q666*	ENST00000302538	NM_021962.3	666	Cag/Tag	0	0.652	TCCACACACTGCCGGACGATG
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7577157	7577157	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14	11			ENST00000269305.4:c.783-2A>C		p.X261_splice	ENST00000269305	NM_001126112.2			0	0.512	AGATTACCACTACTCAGGATA
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40	45			ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	0	0.572	GTTACACATGTAGTTGTAGTG
HS3ST3A1	9955	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	13400056	13400056	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	177	53			ENST00000284110.1:c.679G>A	p.Ala227Thr	p.A227T	ENST00000284110	NM_006042.1	227	Gcg/Acg	0	0.627	GAGATGCGCGCGGGGGCCTCC
SH2D1B	117157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	162381781	162381781	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79	10			ENST00000367929.2:c.26G>A	p.Arg9His	p.R9H	ENST00000367929	NM_053282.4	9	cGt/cAt	0	0.532	CTTGGTCAGACGTCCATGGTA
OR2M3	127062	hgsc.bcm.edu;broad.mit.edu	GRCh37	1	248366698	248366698	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	300	22			ENST00000456743.1:c.329C>G	p.Ser110Cys	p.S110C	ENST00000456743	NM_001004689.1	110	tCt/tGt	0	0.458	CTGCTTGGCTCTGAGTGCTTT
SSTR3	6753	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	22	37603530	37603530	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	80	54			ENST00000328544.3:c.313G>A	p.Ala105Thr	p.A105T	ENST00000328544	NM_001051.3	105	Gcc/Acc	0	0.622	TAGGACAGGGCGTTCTGGGCG
MPPED1	758	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	22	43898541	43898541	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	158	17			ENST00000417669.2:c.766C>A	p.Pro256Thr	p.P256T	ENST00000417669		256	Ccc/Acc	0	0.632	GGACTGGGTCCCCAAGAAGAT
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	53	16			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
SEC61A1	29927	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	127786281	127786281	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	111	59			ENST00000243253.3:c.993C>T	p.Gly331=	p.G331=	ENST00000243253	NM_013336.3	331	ggC/ggT	0	0.483	CTTCTGGGGGCCCAGCACGTG
PIK3R4	30849	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	130463923	130463923	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42	18			ENST00000356763.3:c.140A>G	p.Glu47Gly	p.E47G	ENST00000356763	NM_014602.2	47	gAa/gGa	0	0.408	GACCAGGCCTTCTCGGTGCTT
SMIM43	132332	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	122681459	122681459	+	missense_variant	Missense_Mutation	SNP	T	T	A			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	31	16			ENST00000337677.5:c.383A>T	p.Lys128Met	p.K128M	ENST00000337677	NM_152399.2	128	aAg/aTg	0	0.403	tcagacaatcttgcagatagc
HOXA7	3204	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	27196035	27196035	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	160	25			ENST00000242159.3:c.130G>A	p.Ala44Thr	p.A44T	ENST00000242159	NM_006896.3	44	Gcc/Acc	0	0.607	AAGGCGCCGGCGCCCGCCCCG
LETM2	137994	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	38262000	38262000	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67	11			ENST00000523983.2:c.1053G>A	p.Pro351=	p.P351=	ENST00000523983		351	ccG/ccA	0	0.557	AGCCCAAGCCGATTGAGATAC
XKR4	114786	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	56436610	56436610	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73	37			ENST00000327381.6:c.1777T>C	p.Ser593Pro	p.S593P	ENST00000327381	NM_052898.1	593	Tca/Cca	0	0.488	GATTGAAGAATCAGTCATTAA
FAM154A	158297	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	18928550	18928550	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68	52			ENST00000380534.4:c.925G>A	p.Ala309Thr	p.A309T	ENST00000380534	NM_153707.2	309	Gcc/Acc	0	0.547	GTGTAATGGGCCTGCACTGTT
ZNF81	347344	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	47774744	47774744	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	85	9			ENST00000376954.1:c.699T>C	p.Tyr233=	p.Y233=	ENST00000376954		233	taT/taC	0	0.363	ACTCTTCTTATAGTCACCACG
GRIPAP1	56850	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	48831681	48831681	+	synonymous_variant	Silent	SNP	C	C	G			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40	22			ENST00000376441.1:c.2319G>C	p.Leu773=	p.L773=	ENST00000376441	NM_020137.3	773	ctG/ctC	0	0.607	GGACGCTGCCCAGCCCGCTGC
RGAG4	340526	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	71350423	71350423	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	129	66			ENST00000545866.1:c.968G>A	p.Arg323Gln	p.R323Q	ENST00000545866	NM_001024455.3	323	cGa/cAa	0	0.493	GATGATATTTCGAACTCCAGG
CSTF2	1478	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	100077401	100077401	+	missense_variant	Missense_Mutation	SNP	A	A	T			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	48	21			ENST00000372972.2:c.299A>T	p.Glu100Val	p.E100V	ENST00000372972	NM_001325.2	100	gAg/gTg	0	0.418	AACAAAGAAGAGCTGAAGAGT
DRP2	1821	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	100490939	100490939	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	211	103			ENST00000395209.3:c.208G>A	p.Ala70Thr	p.A70T	ENST00000395209	NM_001939.2	70	Gcc/Acc	0	0.517	GTCTGTTGGTGCCTCTGGACC
SERPINA7	6906	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	105280487	105280487	+	missense_variant	Missense_Mutation	SNP	A	A	C			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	116	60			ENST00000327674.4:c.563T>G	p.Leu188Arg	p.L188R	ENST00000327674		188	cTa/cGa	0	0.413	GTCTTGAATTAGACCCACAAC
DOCK11	139818	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	117773444	117773444	+	missense_variant	Missense_Mutation	SNP	T	T	A			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	103	17			ENST00000276202.7:c.4048T>A	p.Ser1350Thr	p.S1350T	ENST00000276202	NM_144658.3	1350	Tcg/Acg	0	0.413	AGACCGAAAATCGCAAACCAT
GPR112	139378	hgsc.bcm.edu;broad.mit.edu	GRCh37	X	135428469	135428469	+	synonymous_variant	Silent	SNP	G	G	C			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	251	22			ENST00000394143.1:c.2604G>C	p.Leu868=	p.L868=	ENST00000394143	NM_153834.3	868	ctG/ctC	0	0.398	CAACAATGCTGGAAGTGACAG
NAA10	8260	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	153195616	153195616	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	89	74			ENST00000464845.1:c.532A>G	p.Asn178Asp	p.N178D	ENST00000464845	NM_003491.3	178	Aac/Gac	0	0.627	TCCACCTTGTTCTCGATGGCA
TAZ	6901	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	153640435	153640435	+	missense_variant	Missense_Mutation	SNP	A	A	T			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	16	17			ENST00000299328.5:c.122A>T	p.His41Leu	p.H41L	ENST00000299328	NM_000116.3	41	cAc/cTc	0	0.677	TACATGAACCACCTGACCGTG
LATS2	26524	broad.mit.edu;ucsc.edu	GRCh37	13	21562142	21562142	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	107	18			ENST00000382592.4:c.1777C>T	p.Arg593Cys	p.R593C	ENST00000382592	NM_014572.2	593	Cgc/Tgc	0	0.512	CTCTTGATGCGTGACTCTCTC
OGT	8473	broad.mit.edu;ucsc.edu	GRCh37	X	70776956	70776956	+	splice_donor_variant	Splice_Site	SNP	G	G	T			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33	4			ENST00000373719.3:c.1320+1G>T		p.X440_splice	ENST00000373719	NM_181673.2			0	0.368	CATTCATAAGGTACTACTGTT
CPZ	8532	broad.mit.edu;ucsc.edu	GRCh37	4	8603122	8603122	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-FG-A60J-01	TCGA-FG-A60J-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10	5			ENST00000360986.4:c.394G>A	p.Ala132Thr	p.A132T	ENST00000360986	NM_001014447.2	132	Gcc/Acc	0	0.677	CTGCCAGCCCGCCTTCGACGC
SVIL	6840	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	29770516	29770516	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-DB-5278-01	TCGA-DB-5278-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	365	192			ENST00000375398.2:c.5097C>A	p.His1699Gln	p.H1699Q	ENST00000375398		1699	caC/caA	0	0.463	GGAATACCTTGTGCTGGGCAA
SLC7A9	11136	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	33355655	33355655	+	missense_variant	Missense_Mutation	SNP	T	T	G			TCGA-DB-5278-01	TCGA-DB-5278-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64	83			ENST00000023064.4:c.115A>C	p.Ile39Leu	p.I39L	ENST00000023064	NM_014270.4	39	Atc/Ctc	0	0.622	GTGCCCACGATGATGGAGATG
CIC	23152	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	42791743	42791743	+	missense_variant	Missense_Mutation	SNP	T	T	G			TCGA-DB-5278-01	TCGA-DB-5278-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	38	39			ENST00000575354.2:c.629T>G	p.Phe210Cys	p.F210C	ENST00000575354	NM_015125.3	210	tTc/tGc	0	0.627	TTCATGATCTTCAGCAAGCGG
RAB3GAP2	25782	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	220387224	220387224	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DB-5278-01	TCGA-DB-5278-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58	25			ENST00000358951.2:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000358951	NM_012414.3	93	cGa/cAa	0	0.363	TTTTTGCTCTCGAGCTATCAC
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-DB-5278-01	TCGA-DB-5278-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	72	46			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
GIMAP6	474344	broad.mit.edu;ucsc.edu	GRCh37	7	150325310	150325310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138521615	byFrequency	TCGA-DB-5278-01	TCGA-DB-5278-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84	36			ENST00000328902.5:c.376G>A	p.Val126Met	p.V126M	ENST00000328902	NM_024711.5	126	Gtg/Atg	0	0.622	ACCAGGAGCACGGCGTGGGGC
CIC	23152	broad.mit.edu	GRCh37	19	42799060	42799060	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DB-5278-01	TCGA-DB-5278-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	46	4			ENST00000575354.2:c.4544G>A	p.Arg1515His	p.R1515H	ENST00000575354	NM_015125.3	1515	cGc/cAc	0	0.632	CGTGAGGTGCGCCAGAAGATC
CTSG	1511	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	14	25043508	25043508	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DU-6404-01	TCGA-DU-6404-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	20	19			ENST00000216336.2:c.537C>T	p.Tyr179=	p.Y179=	ENST00000216336	NM_001911.2	179	taC/taT	0	0.627	TTCGGGGGTCGTAGGAACCGA
FPR1	2357	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	52250087	52250087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145808420		TCGA-DU-6404-01	TCGA-DU-6404-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24	18			ENST00000595042.1:c.161G>A	p.Arg54Gln	p.R54Q	ENST00000595042	NM_001193306.1	54	cGg/cAg	0	0.527	GTGTGTCATCCGGAATCCAGC
FMNL2	114793	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	153473700	153473700	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-DU-6404-01	TCGA-DU-6404-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28	18			ENST00000288670.9:c.1308C>T	p.Val436=	p.V436=	ENST00000288670	NM_052905.3	436	gtC/gtT	0	0.473	AGCTGGATGTCGTTCGGGTAA
ACOX3	8310	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	8396382	8396382	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs142042116		TCGA-DU-6404-01	TCGA-DU-6404-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10	17			ENST00000356406.5:c.1144C>T	p.Arg382Ter	p.R382*	ENST00000356406	NM_003501.2	382	Cga/Tga	0	0.542	GCAAGTCCTCGCTGGAGCTCC
SPP1	6696	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	88901213	88901213	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-6404-01	TCGA-DU-6404-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	65	26			ENST00000395080.3:c.109C>T	p.Pro37Ser	p.P37S	ENST00000395080	NM_001040058.1	37	Cca/Tca	0	0.363	CAACAAATACCCAGATGCTGT
TRO	7216	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	54953051	54953051	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-6404-01	TCGA-DU-6404-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	83	55			ENST00000173898.7:c.1693C>T	p.Arg565Cys	p.R565C	ENST00000173898	NM_001039705.2	565	Cgc/Tgc	0	0.577	GTTGGGGCTGCGCCCTGGGTA
GDPD2	54857	hgsc.bcm.edu;broad.mit.edu	GRCh37	X	69652187	69652187	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-DU-6404-01	TCGA-DU-6404-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	148	12			ENST00000453994.2:c.1491C>A	p.Asn497Lys	p.N497K	ENST00000453994	NM_001171192.1	497	aaC/aaA	0	0.527	TCTCGGTGAACCTATTTGTAG
TRBV11-1	28582	broad.mit.edu;ucsc.edu	GRCh37	7	142224222	142224222	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-DU-6404-01	TCGA-DU-6404-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	32	20			ENST00000390367.3:c.46G>T	p.Ala16Ser	p.A16S	ENST00000390367		16	Gca/Tca	0	0.498	GACACACCTGCCCCCAGGAGA
G6PD	2539	broad.mit.edu;ucsc.edu	GRCh37	X	153761826	153761826	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-6404-01	TCGA-DU-6404-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	34	4			ENST00000393562.2:c.919G>A	p.Ala307Thr	p.A307T	ENST00000393562	NM_000402.3	307	Gcc/Acc	0	0.637	TTGGTGGAGGCGGGCTTCTCC
SLC25A19	60386	broad.mit.edu;ucsc.edu	GRCh37	17	73282427	73282427	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DU-6404-01	TCGA-DU-6404-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	80	40			ENST00000402418.3:c.246C>T	p.His82=	p.H82=	ENST00000402418		82	caC/caT	0	0.592	GAGCTGGGACGTGTCCTTTCC
ATG5	9474	broad.mit.edu;ucsc.edu	GRCh37	6	106764059	106764059	+	stop_gained	Nonsense_Mutation	SNP	G	G	A			TCGA-DU-6404-01	TCGA-DU-6404-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	72	43			ENST00000369076.3:c.25C>T	p.Arg9Ter	p.R9*	ENST00000369076	NM_004849.2	9	Cga/Tga	0	0.368	CACACATCTCGAAGCACATCT
KLHL13	90293	broad.mit.edu;ucsc.edu	GRCh37	X	117043975	117043975	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-6404-01	TCGA-DU-6404-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	120	20			ENST00000539496.1:c.664G>A	p.Val222Ile	p.V222I	ENST00000539496	NM_001168299.1	222	Gtc/Atc	0	0.423	TTCTTCAAGACGAAACTGTTA
KALRN	8997	broad.mit.edu;ucsc.edu	GRCh37	3	124053129	124053129	+	missense_variant	Missense_Mutation	SNP	A	A	C			TCGA-DU-6404-01	TCGA-DU-6404-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75	38			ENST00000240874.3:c.1428A>C	p.Lys476Asn	p.K476N	ENST00000240874	NM_003947.4	476	aaA/aaC	0	0.572	AGGATGGCAAAGCACTACTTG
MAGI3	260425	broad.mit.edu;ucsc.edu	GRCh37	1	114123223	114123223	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-6404-01	TCGA-DU-6404-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	77	20			ENST00000307546.9:c.493G>A	p.Val165Ile	p.V165I	ENST00000307546	NM_001142782.1	165	Gtt/Att	0	0.393	TTTCATTTCCGTTGAACAGTT
PWWP2B	170394	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	134218474	134218474	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-QH-A65V-01	TCGA-QH-A65V-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23	14			ENST00000305233.5:c.470G>A	p.Arg157His	p.R157H	ENST00000305233	NM_138499.3	157	cGc/cAc	0	0.726	CGTCTGTCCCGCAACCGCGAC
OR5AS1	219447	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	55798589	55798589	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-QH-A65V-01	TCGA-QH-A65V-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	115	67			ENST00000313555.1:c.695G>T	p.Gly232Val	p.G232V	ENST00000313555	NM_001001921.1	232	gGt/gTt	0	0.453	AAGTCCTCAGGTGGCAGAAGC
ZC3H13	23091	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	13	46619598	46619598	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-QH-A65V-01	TCGA-QH-A65V-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	107	53			ENST00000282007.3:c.45T>C	p.Thr15=	p.T15=	ENST00000282007	NM_015070.3	15	acT/acC	0	0.413	TATCAGATATAGTCTTGGTAT
C15orf43	145645	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	45248953	45248953	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-QH-A65V-01	TCGA-QH-A65V-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	87	33			ENST00000340827.3:c.37G>A	p.Val13Ile	p.V13I	ENST00000340827	NM_152448.2	13	Gtt/Att	0	0.582	TTGCGGCAGCGTTAGCCAGGA
LONP2	83752	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	48296697	48296697	+	missense_variant	Missense_Mutation	SNP	A	A	C			TCGA-QH-A65V-01	TCGA-QH-A65V-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21	9			ENST00000285737.4:c.896A>C	p.Lys299Thr	p.K299T	ENST00000285737	NM_031490.2	299	aAa/aCa	0	0.348	AGACTCAAAAAAATGCCTCAG
PSME3	10197	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	40990763	40990763	+	stop_gained	Nonsense_Mutation	SNP	C	C	T			TCGA-QH-A65V-01	TCGA-QH-A65V-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	55	31			ENST00000293362.3:c.460C>T	p.Gln154Ter	p.Q154*	ENST00000293362	NM_176863.2	154	Cag/Tag	0	0.463	AATGTGGGTACAGCTCCTGAT
KCNAB2	8514	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	6155592	6155592	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T			TCGA-QH-A65V-01	TCGA-QH-A65V-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42	48			ENST00000378083.3:c.856G>T	p.Val286Leu	p.V286L	ENST00000378083	NM_001199862.1	286	Gtg/Ttg	0	0.632	CTCTTCAGGAGTGGGCGCCAT
CD40	958	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	20	44751286	44751286	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-QH-A65V-01	TCGA-QH-A65V-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	87	41			ENST00000372285.3:c.294A>G	p.Glu98=	p.E98=	ENST00000372285	NM_001250.4	98	gaA/gaG	0	0.607	GCACCTCAGAAACAGACACCA
NCKAP1	10787	hgsc.bcm.edu;broad.mit.edu	GRCh37	2	183866755	183866755	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-QH-A65V-01	TCGA-QH-A65V-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	80	8			ENST00000360982.2:c.547C>T	p.Arg183Cys	p.R183C	ENST00000360982	NM_013436.4	183	Cgc/Tgc	0	0.363	TGGCCAAGGCGTGGGTATTCT
ZC3H15	55854	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	187371527	187371527	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-QH-A65V-01	TCGA-QH-A65V-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67	24			ENST00000337859.6:c.1054C>G	p.Leu352Val	p.L352V	ENST00000337859	NM_018471.2	352	Ctt/Gtt	0	0.348	TGTAGCCAGTCTTGAAAGATT
COL5A2	1290	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	189898826	189898826	+	synonymous_variant	Silent	SNP	G	G	A	rs142895373		TCGA-QH-A65V-01	TCGA-QH-A65V-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	56	24			ENST00000374866.3:c.4470C>T	p.Gly1490=	p.G1490=	ENST00000374866	NM_000393.3	1490	ggC/ggT	0	0.473	CAATTTCAACGCCGAATTCCT
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-QH-A65V-01	TCGA-QH-A65V-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47	23			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
SCAND3	114821	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	28540332	28540332	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-QH-A65V-01	TCGA-QH-A65V-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42	20			ENST00000452236.2:c.3334T>C	p.Phe1112Leu	p.F1112L	ENST00000452236	NM_052923.1	1112	Ttt/Ctt	0	0.353	agatcattaaaaatactgaag
PCLO	27445	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	82578793	82578793	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A			TCGA-QH-A65V-01	TCGA-QH-A65V-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	171	68			ENST00000333891.9:c.11111C>T	p.Thr3704Met	p.T3704M	ENST00000333891	NM_033026.5	3704	aCg/aTg	0	0.463	CACTCTTACCGTATAGCCCTC
SND1	27044	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	127631024	127631024	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-QH-A65V-01	TCGA-QH-A65V-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29	13			ENST00000354725.3:c.1694G>A	p.Arg565Gln	p.R565Q	ENST00000354725	NM_014390.2	565	cGa/cAa	0	0.542	AGAGGAGCCCGAAACCTCCCA
TNC	3371	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	117848575	117848575	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-QH-A65V-01	TCGA-QH-A65V-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	201	92			ENST00000350763.4:c.1435C>T	p.Arg479Cys	p.R479C	ENST00000350763	NM_002160.3	479	Cgc/Tgc	0	0.582	TTCACACAGCGGCCGTGCTGG
MID1IP1	58526	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	38664318	38664318	+	missense_variant	Missense_Mutation	SNP	A	A	T			TCGA-QH-A65V-01	TCGA-QH-A65V-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	53	32			ENST00000336949.6:c.119A>T	p.Asp40Val	p.D40V	ENST00000336949	NM_021242.4	40	gAc/gTc	0	0.632	TTGCTGCGCGACGTGCCCCTG
NOTCH2	4853	broad.mit.edu;ucsc.edu	GRCh37	1	120491184	120491184	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-QH-A65V-01	TCGA-QH-A65V-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	33	29			ENST00000256646.2:c.2605C>T	p.Arg869Trp	p.R869W	ENST00000256646	NM_024408.3	869	Cgg/Tgg	0	0.512	ATGGTACACCGCTGACCTAGG
UNC13D	201294	broad.mit.edu;ucsc.edu	GRCh37	17	73826535	73826535	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-QH-A65V-01	TCGA-QH-A65V-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9	5			ENST00000207549.4:c.2738C>T	p.Ala913Val	p.A913V	ENST00000207549	NM_199242.2	913	gCt/gTt	0	0.682	GACTGTCACAGCCCCCAGCTC
TRPV6	55503	broad.mit.edu;ucsc.edu	GRCh37	7	142571891	142571891	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-QH-A65V-01	TCGA-QH-A65V-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37	5			ENST00000359396.3:c.1457T>C	p.Ile486Thr	p.I486T	ENST00000359396	NM_018646.4	486	aTt/aCt	0	0.547	GTCGCCAAAAATCATCTAGAA
HYLS1	219844	broad.mit.edu;ucsc.edu	GRCh37	11	125770123	125770123	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-QH-A65V-01	TCGA-QH-A65V-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45	28			ENST00000425380.2:c.860T>C	p.Val287Ala	p.V287A	ENST00000425380	NM_001134793.1	287	gTc/gCc	0	0.403	GCAAATGGTGTCATACCCAGG
STAG3L4	64940	broad.mit.edu;ucsc.edu	GRCh37	7	66771046	66771046	+	non_coding_transcript_exon_variant	RNA	SNP	T	T	G			TCGA-QH-A65V-01	TCGA-QH-A65V-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84	52			ENST00000416602.2:n.338T>G		*113*	ENST00000416602				0	0.388	TGTTAACTTTTTCATCTGATC
CIC	23152	broad.mit.edu;ucsc.edu	GRCh37	19	42799059	42799059	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-QH-A65V-01	TCGA-QH-A65V-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	51	23			ENST00000575354.2:c.4543C>T	p.Arg1515Cys	p.R1515C	ENST00000575354	NM_015125.3	1515	Cgc/Tgc	0	0.632	CCGTGAGGTGCGCCAGAAGAT
XG	7499	broad.mit.edu;hgsc.bcm.edu	GRCh37	X	2670333	2670333	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-			TCGA-QH-A65V-01	TCGA-QH-A65V-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	127	47			ENST00000419513.2:c.18delA	p.Leu7PhefsTer10	p.L7Ffs*10	ENST00000419513	NM_001141919.1	6	ggA/gg	0	0.532	GCTGGTGGGGACTTCCCTGTC
OR10A4	283297	hgsc.bcm.edu;broad.mit.edu	GRCh37	11	6898019	6898019	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-DU-8163-01	TCGA-DU-8163-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	143	10			ENST00000379829.2:c.141C>G	p.Ile47Met	p.I47M	ENST00000379829	NM_207186.2	47	atC/atG	0	0.453	TCCTCATCATCCTGGTCACTA
GLI1	2735	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	57861814	57861814	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-8163-01	TCGA-DU-8163-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	114	12			ENST00000228682.2:c.1115G>A	p.Arg372His	p.R372H	ENST00000228682	NM_005269.2	372	cGc/cAc	0	0.542	TGCACCAAACGCTATACAGAT
TJP1	7082	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	30001004	30001004	+	stop_gained	Nonsense_Mutation	SNP	G	G	A			TCGA-DU-8163-01	TCGA-DU-8163-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	202	82			ENST00000346128.6:c.4609C>T	p.Arg1537Ter	p.R1537*	ENST00000346128	NM_175610.2	1537	Cga/Tga	0	0.403	TCAAATGGTCGGGCAGAACTT
GCNT3	9245	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	59911328	59911328	+	synonymous_variant	Silent	SNP	G	G	A	rs139760962		TCGA-DU-8163-01	TCGA-DU-8163-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	173	25			ENST00000396065.1:c.891G>A	p.Ala297=	p.A297=	ENST00000396065	NM_004751.2	297	gcG/gcA	0	0.408	CAGGGAATGCGTACATTGTGG
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	by1000genomes	TCGA-DU-8163-01	TCGA-DU-8163-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11	15			ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	0	0.542	GGCACAAACACGCACCTCAAA
MAPK7	5598	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	19283952	19283952	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-DU-8163-01	TCGA-DU-8163-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	112	20			ENST00000308406.5:c.430C>G	p.Leu144Val	p.L144V	ENST00000308406	NM_139033.2	144	Ctg/Gtg	0	0.582	GGAAAGCGACCTGCACCAGAT
MAPK7	5598	hgsc.bcm.edu;broad.mit.edu	GRCh37	17	19284535	19284535	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-8163-01	TCGA-DU-8163-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	81	6			ENST00000308406.5:c.1013C>T	p.Ala338Val	p.A338V	ENST00000308406	NM_139033.2	338	gCa/gTa	0	0.622	CGCATCTCAGCAGCTGCTGCC
MYO18A	399687	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	27434129	27434129	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-8163-01	TCGA-DU-8163-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	150	52			ENST00000527372.1:c.3410G>A	p.Gly1137Glu	p.G1137E	ENST00000527372	NM_078471.3	1137	gGg/gAg	0	0.612	GTAGTTACGCCCGTGTTTCTT
CLCNKA	1187	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	16352610	16352610	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-DU-8163-01	TCGA-DU-8163-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	433	67			ENST00000331433.4:c.366A>G	p.Gly122=	p.G122=	ENST00000331433		122	ggA/ggG	0	0.552	AAGGTTCTGGAATCCCGGAGC
CAPN2	824	hgsc.bcm.edu;broad.mit.edu	GRCh37	1	223900426	223900426	+	synonymous_variant	Silent	SNP	C	C	G			TCGA-DU-8163-01	TCGA-DU-8163-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	20	11			ENST00000295006.5:c.84C>G	p.Leu28=	p.L28=	ENST00000295006	NM_001748.4	28	ctC/ctG	0	0.716	TCAAGTACCTCAACCAGGACT
OR2T12	127064	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	248458716	248458716	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-DU-8163-01	TCGA-DU-8163-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41	8			ENST00000317996.1:c.165G>A	p.Arg55=	p.R55=	ENST00000317996	NM_001004692.1	55	agG/agA	0	0.527	AGTACATGGGCCTGTGGAGCC
DYNC2LI1	51626	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	44028017	44028017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141895414		TCGA-DU-8163-01	TCGA-DU-8163-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	48	6			ENST00000260605.8:c.692G>A	p.Arg231His	p.R231H	ENST00000260605	NM_001193464.1	231	cGt/cAt	0	0.313	CTAAAAATACGTGGAGTTATC
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-DU-8163-01	TCGA-DU-8163-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79	26			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
XIRP1	165904	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	39227182	39227182	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-8163-01	TCGA-DU-8163-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	27	10			ENST00000340369.3:c.3755C>T	p.Ala1252Val	p.A1252V	ENST00000340369	NM_194293.2	1252	gCc/gTc	0	0.622	AGGAACAAAGGCATTATGGGG
RUNX2	860	hgsc.bcm.edu;broad.mit.edu	GRCh37	6	45390466	45390466	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-DU-8163-01	TCGA-DU-8163-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36	4			ENST00000371438.1:c.195A>G	p.Gln65=	p.Q65=	ENST00000371438	NM_001024630.3	65	caA/caG	0	0.731	agcagcagcaacagcagcagc
ATRX	546	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	76814188	76814188	+	stop_gained	Nonsense_Mutation	SNP	A	A	C			TCGA-DU-8163-01	TCGA-DU-8163-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45	10			ENST00000373344.5:c.6456T>G	p.Tyr2152Ter	p.Y2152*	ENST00000373344	NM_000489.3	2152	taT/taG	0	0.338	GTCCAAAGCGATAAACTCTGA
ATRX	546	hgsc.bcm.edu;ucsc.edu	GRCh37	X	76944328	76944328	+	stop_gained	Nonsense_Mutation	SNP	G	G	A			TCGA-DU-8163-01	TCGA-DU-8163-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37	10			ENST00000373344.5:c.577C>T	p.Gln193Ter	p.Q193*	ENST00000373344	NM_000489.3	193	Caa/Taa	0	0.383	ATAAGAACTTGCAATGAAGGG
PCDH15	65217	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	55581631	55581631	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	125	23			ENST00000361849.3:c.5861C>G	p.Ser1954Cys	p.S1954C	ENST00000361849	NM_001142768.1	1954	tCt/tGt	0	0.363	CAGTGAAGTAGATTGACTGTG
OR6Q1	219952	hgsc.bcm.edu;broad.mit.edu	GRCh37	11	57798711	57798711	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	149	10			ENST00000302622.3:c.287T>C	p.Ile96Thr	p.I96T	ENST00000302622	NM_001005186.2	96	aTc/aCc	0	0.483	GGCAAGAATATCTCTTATGCT
COQ5	84274	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	120947837	120947837	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45	15			ENST00000288532.6:c.664G>A	p.Val222Ile	p.V222I	ENST00000288532	NM_032314.3	222	Gtc/Atc	0	0.433	ATGTGTGTGACATTCCGGATC
CEBPE	1053	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	14	23588124	23588124	+	synonymous_variant	Silent	SNP	G	G	A	rs141320203		TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	163	28			ENST00000206513.5:c.177C>T	p.Ala59=	p.A59=	ENST00000206513	NM_001805.3	59	gcC/gcT	0	0.647	CTGGCTTCACGGCAAAGAGAT
OTX2	5015	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	14	57268721	57268721	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	83	22			ENST00000339475.5:c.626G>T	p.Cys209Phe	p.C209F	ENST00000339475	NM_001270524.1	209	tGt/tTt	0	0.522	ATATGATCCACAGTCCATGCC
PLIN1	5346	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	90212791	90212791	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71	23			ENST00000300055.5:c.711G>A	p.Met237Ile	p.M237I	ENST00000300055	NM_002666.4	237	atG/atA	0	0.642	GGGCCCGGGCCATGGTCTGCA
WDR24	84219	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	739166	739166	+	missense_variant	Missense_Mutation	SNP	A	A	T			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	102	44			ENST00000293883.4:c.475T>A	p.Phe159Ile	p.F159I	ENST00000293883	NM_032259.2	159	Ttc/Atc	0	0.632	TCACCCGAGAAGGTGCTGACA
CYP4F12	66002	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	15807863	15807863	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	120	24			ENST00000550308.1:c.1543C>T	p.Arg515Trp	p.R515W	ENST00000550308	NM_023944.3	515	Cgg/Tgg	0	0.567	GCTTTGGCTGCGGGTGGAGCC
ZNF676	163223	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	22363763	22363763	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	66	30			ENST00000397121.2:c.756C>T	p.Pro252=	p.P252=	ENST00000397121	NM_001001411.2	252	ccC/ccT	0	0.373	CACATTTGTAGGGTTTCTCTC
ZNF644	84146	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	91405999	91405999	+	synonymous_variant	Silent	SNP	G	G	T	rs144274015	byFrequency	TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30	10			ENST00000370440.1:c.912C>A	p.Thr304=	p.T304=	ENST00000370440		304	acC/acA	0	0.343	AGCAATCCTCGGTATAACGAG
INSRR	3645	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	156815851	156815851	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	85	18			ENST00000368195.3:c.1871G>A	p.Arg624His	p.R624H	ENST00000368195	NM_014215.2	624	cGc/cAc	0	0.622	TGGCTTCCAGCGCACCAGGAG
FCRL2	79368	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	157738222	157738222	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	104	19			ENST00000361516.3:c.865G>A	p.Val289Met	p.V289M	ENST00000361516	NM_030764.3	289	Gtg/Atg	0	0.478	GGGATATTCACCACCTTGCTC
ABL2	27	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	179084144	179084144	+	missense_variant	Missense_Mutation	SNP	T	T	A			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	105	20			ENST00000502732.1:c.1430A>T	p.Glu477Val	p.E477V	ENST00000502732	NM_001168237.1	477	gAa/gTa	0	0.378	GGTAGCAATTTCCCACAACAA
RD3	343035	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	211652456	211652456	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29	6			ENST00000367002.4:c.510C>T	p.Ser170=	p.S170=	ENST00000367002	NM_001164688.1	170	tcC/tcT	0	0.716	CCACGTCCTCGGAGATGGTCC
CHRM3	1131	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	240071128	240071128	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39	20			ENST00000255380.4:c.377C>T	p.Thr126Met	p.T126M	ENST00000255380	NM_000740.2	126	aCg/aTg	0	0.468	AATCTGTTTACGACCTACATC
CHAF1B	8208	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	21	37775114	37775114	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	265	55			ENST00000314103.5:c.722G>C	p.Ser241Thr	p.S241T	ENST00000314103	NM_005441.2	241	aGt/aCt	0	0.443	CGTAGACTGAGTTTCACTCCC
MORC2	22880	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	22	31330834	31330834	+	synonymous_variant	Silent	SNP	A	A	C			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	220	70			ENST00000215862.4:c.1941T>G	p.Val647=	p.V647=	ENST00000215862	NM_014941.1	647	gtT/gtG	0	0.552	TGGGAGAAGGAACCTCCCGAG
NLRC4	58484	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	32449596	32449596	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75	47			ENST00000404025.2:c.3021T>C	p.Phe1007=	p.F1007=	ENST00000404025		1007	ttT/ttC	0	0.378	CATCATCATCAAATTGCCACC
IFIH1	64135	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	163133214	163133214	+	missense_variant	Missense_Mutation	SNP	A	A	C			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	70	12			ENST00000263642.2:c.2287T>G	p.Phe763Val	p.F763V	ENST00000263642	NM_022168.3	763	Ttc/Gtc	0	0.398	ATGGGTTTGAACTCACTGCTG
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	27	22			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
CCDC13	152206	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	42750573	42750573	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	85	21			ENST00000310232.6:c.2047C>T	p.Arg683Trp	p.R683W	ENST00000310232	NM_144719.3	683	Cgg/Tgg	0	0.592	TCCTTTCCCCGCAGGGCACTG
TRAIP	10293	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	49867117	49867117	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	51	29			ENST00000331456.2:c.1169G>A	p.Arg390Gln	p.R390Q	ENST00000331456	NM_005879.2	390	cGg/cAg	0	0.587	GATGGCATTCCGGACAAAAAT
WDR17	116966	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	177032847	177032847	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39	16			ENST00000280190.4:c.188T>C	p.Ile63Thr	p.I63T	ENST00000280190		63	aTt/aCt	0	0.343	GCTATCTATATTTATCAGGTA
ITPR3	3710	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	33632727	33632727	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	48	25			ENST00000374316.5:c.1229A>G	p.Glu410Gly	p.E410G	ENST00000374316		410	gAg/gGg	0	0.667	ATCGAGGAGGAGCGGCCCATC
PKHD1	5314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	51768522	51768522	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45	18			ENST00000371117.3:c.6869G>C	p.Trp2290Ser	p.W2290S	ENST00000371117	NM_138694.3	2290	tGg/tCg	0	0.393	ATGTCCTGACCAGTCTAATGT
TNS3	64759	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	47407972	47407972	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258	74			ENST00000398879.1:c.2271C>T	p.Thr757=	p.T757=	ENST00000398879		757	acC/acT	0	0.632	CTTGCCGCCCGGTGGCCCTGC
COBL	23242	hgsc.bcm.edu;ucsc.edu	GRCh37	7	51093066	51093066	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69	14			ENST00000265136.7:c.3508G>A	p.Ala1170Thr	p.A1170T	ENST00000265136	NM_015198.3	1170	Gca/Aca	0	0.517	GCAGAGGATGCCACCTGGCAA
CYP3A4	1576	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	99364768	99364768	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	51	15			ENST00000336411.2:c.784G>A	p.Glu262Lys	p.E262K	ENST00000336411	NM_001202855.2	262	Gaa/Aaa	0	0.308	TGTGTATCTTCGAGGCGACTT
PTPRZ1	5803	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	121693973	121693973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82	51			ENST00000393386.2:c.6262C>T	p.Gln2088Ter	p.Q2088*	ENST00000393386	NM_001206838.1	2088	Cag/Tag	0	0.403	GGGCTATTACCAGAGCAATGA
CRISPLD1	83690	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	75932115	75932115	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23	24			ENST00000262207.4:c.1138T>C	p.Ser380Pro	p.S380P	ENST00000262207	NM_031461.5	380	Tct/Cct	0	0.333	CAAATATCAGTCTGCTAATTC
SPATA31C1	441452	hgsc.bcm.edu;broad.mit.edu	GRCh37	9	90535986	90535986	+	non_coding_transcript_exon_variant	RNA	SNP	G	G	A			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	356	66			ENST00000420021.2:n.1461G>A		*487*	ENST00000420021				0	0.517	GCCCTGCGTCGCAGAATAAAG
RGS3	5998	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	116224037	116224037	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	125	26			ENST00000374140.2:c.131G>A	p.Arg44His	p.R44H	ENST00000374140	NM_144488.5	44	cGt/cAt	0	0.537	GGATCTCACCGTCCTGAGTGT
KIF2B	84643	broad.mit.edu;ucsc.edu	GRCh37	17	51902246	51902246	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	109	24			ENST00000268919.4:c.1852C>A	p.Gln618Lys	p.Q618K	ENST00000268919	NM_032559.4	618	Caa/Aaa	0	0.443	GGGATCTAGCCAATGGCTGGA
MAP2K5	5607	broad.mit.edu;ucsc.edu	GRCh37	15	67878228	67878228	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78	9			ENST00000178640.5:c.323C>T	p.Ala108Val	p.A108V	ENST00000178640	NM_145160.2	108	gCc/gTc	0	0.373	ACTGTTTCAGCCTGCAAGCCT
APIP	51074	broad.mit.edu;ucsc.edu	GRCh37	11	34909891	34909891	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74	22			ENST00000395787.3:c.410A>G	p.His137Arg	p.H137R	ENST00000395787	NM_015957.2	137	cAt/cGt	0	0.373	CATCTCTTGATGTGTAATTTT
PCDHB4	56131	broad.mit.edu;ucsc.edu	GRCh37	5	140502918	140502918	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	117	115			ENST00000194152.1:c.1338C>T	p.Asn446=	p.N446=	ENST00000194152	NM_018938.2	446	aaC/aaT	0	0.602	TCAATGACAACGCCCCCGCCT
NOTCH1	4851	broad.mit.edu;ucsc.edu	GRCh37	9	139412302	139412302	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	83	24			ENST00000277541.6:c.1343G>T	p.Arg448Leu	p.R448L	ENST00000277541	NM_017617.3	448	cGa/cTa	0	0.647	GATCTCGCATCGGGGGCCCGT
EIF4G3	8672	broad.mit.edu;hgsc.bcm.edu	GRCh37	1	21183987	21183987	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	222	51			ENST00000602326.1:c.3098delT	p.Val1033AlafsTer27	p.V1033Afs*27	ENST00000602326	NM_001198802.1	1033	gTc/gc	0	0.463	CACTCTCTGGACACCTGCAGG
ATF2	1386	broad.mit.edu;hgsc.bcm.edu	GRCh37	2	175957831	175957833	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95	38			ENST00000264110.2:c.1141_1143delGAG	p.Glu381del	p.E381del	ENST00000264110	NM_001256091.1	381	GAG/-	0	0.35	CAGCTTTCTTCTCTAAAGACTGA
SCRIB	23513	broad.mit.edu;hgsc.bcm.edu	GRCh37	8	144886879	144886882	+	frameshift_variant	Frame_Shift_Del	DEL	GGGA	GGGA	-			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30	10			ENST00000356994.2:c.2865_2868delTCCC	p.Pro956AlafsTer18	p.P956Afs*18	ENST00000356994	NM_182706.4	955	ccTCCC/cc	0	0.696	GCAGAGGGCTGGGAGGAAGAGGGC
MALAT1	378938	broad.mit.edu;hgsc.bcm.edu	GRCh37	11	65270886	65270887	+	non_coding_transcript_exon_variant	RNA	INS	-	-	TA			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	53	12			ENST00000534336.1:n.5655_5656dupTA		*1885*	ENST00000534336				0	0.371	ATTTGCATCTTTAAATAATTTC
RXFP2	122042	broad.mit.edu;hgsc.bcm.edu	GRCh37	13	32371470	32371471	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52	45			ENST00000298386.2:c.1920_1921delCT	p.Phe642TyrfsTer5	p.F642Yfs*5	ENST00000298386	NM_130806.3	640	tTC/t	0	0.396	GCAAATCGTTTCTTTTTTATAG
DNAJA2	10294	broad.mit.edu;hgsc.bcm.edu	GRCh37	16	46991039	46991040	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	304	156			ENST00000317089.5:c.1140_1141delAG	p.Gly381LeufsTer8	p.G381Lfs*8	ENST00000317089	NM_005880.3	380	cgAGgc/cggc	0	0.465	CCTCCTGAGCCTCGAGTGCTAT
TP53	7157	broad.mit.edu;hgsc.bcm.edu	GRCh37	17	7576886	7576887	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21	83			ENST00000269305.4:c.959dupA	p.Lys321GlufsTer16	p.K321Efs*16	ENST00000269305	NM_001126112.2	320	aag/aaAg	0	0.46	CCAGTGGTTTCTTCTTTGGCTG
ATRX	546	broad.mit.edu;hgsc.bcm.edu	GRCh37	X	76938097	76938100	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-			TCGA-DH-A66B-01	TCGA-DH-A66B-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28	79			ENST00000373344.5:c.2648_2651delAAGA	p.Gln883ArgfsTer21	p.Q883Rfs*21	ENST00000373344	NM_000489.3	883	cAAGAg/cg	0	0.407	AGTCTCTCTCTCTTGTTTTCTTTC
LRRC18	474354	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	50122058	50122058	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	54	25			ENST00000374160.3:c.143G>A	p.Arg48His	p.R48H	ENST00000374160	NM_001006939.3	48	cGc/cAc	0	0.507	GTCACTAAGGCGCAGAATACA
CDH23	64072	hgsc.bcm.edu;broad.mit.edu	GRCh37	10	73544798	73544798	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	124	11			ENST00000224721.6:c.5668C>T	p.Arg1890Cys	p.R1890C	ENST00000224721	NM_022124.5	1890	Cgc/Tgc	0	0.602	CTGCAATGCACGCCTCACCTT
CCDC89	220388	hgsc.bcm.edu;broad.mit.edu	GRCh37	11	85397064	85397064	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62	5			ENST00000316398.3:c.110C>T	p.Thr37Met	p.T37M	ENST00000316398	NM_152723.1	37	aCg/aTg	0	0.552	CTTAAACTCCGTCTCCTCTTC
KCNJ1	3758	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	128710111	128710111	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	106	11			ENST00000392664.2:c.85G>A	p.Val29Ile	p.V29I	ENST00000392664	NM_000220.4	29	Gtc/Atc	0	0.408	AAGCGAGTGACGACCCATTTC
VWF	7450	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	6128787	6128787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61749370		TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	51	26			ENST00000261405.5:c.3797C>T	p.Pro1266Leu	p.P1266L	ENST00000261405	NM_000552.3	1266	cCg/cTg	0	0.612	ATCGTGCAACGGCGGTTCCGA
GATC	283459	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	120894951	120894951	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37	19			ENST00000551765.1:c.327C>T	p.Arg109=	p.R109=	ENST00000551765	NM_176818.2	109	cgC/cgT	0	0.478	ACTCCCATCGCGTCGTGGAGG
TGM7	116179	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	43584939	43584939	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97	70			ENST00000452443.2:c.407C>T	p.Thr136Ile	p.T136I	ENST00000452443	NM_052955.2	136	aCt/aTt	0	0.478	TAGGATGAAAGTTCCCAGCGG
ACSBG1	23205	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	78475123	78475123	+	stop_gained	Nonsense_Mutation	SNP	C	C	T			TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40	24			ENST00000258873.4:c.668G>A	p.Trp223Ter	p.W223*	ENST00000258873	NM_001199377.1	223	tGg/tAg	0	0.463	CAACTGTTTCCAGATCTGCAT
TMEM8A	58986	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	427459	427459	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29	14			ENST00000431232.2:c.426C>T	p.Ser142=	p.S142=	ENST00000431232	NM_021259.2	142	tcC/tcT	0	0.677	AAACGTTGACGGAGGCATTGC
CES3	23491	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	66997813	66997813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148620443	byFrequency	TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	77	75			ENST00000303334.4:c.535C>T	p.Arg179Cys	p.R179C	ENST00000303334	NM_024922.5	179	Cgc/Tgc	0	0.607	AGTCCAGTACCGCCTTGGGGT
RFXANK	8625	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	19307810	19307810	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	241	31			ENST00000303088.4:c.226C>T	p.Arg76Trp	p.R76W	ENST00000303088	NM_003721.3	76	Cgg/Tgg	0	0.617	TCTCACCAACCGGCAGCGAGG
FASLG	356	hgsc.bcm.edu;broad.mit.edu	GRCh37	1	172628634	172628634	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	54	5			ENST00000367721.2:c.293G>T	p.Gly98Val	p.G98V	ENST00000367721	NM_000639.1	98	gGc/gTc	0	0.572	GTAGGATTGGGCCTGGGGATG
ADCY3	109	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	25062839	25062839	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	132	18			ENST00000260600.5:c.1258G>A	p.Val420Met	p.V420M	ENST00000260600	NM_004036.3	420	Gtg/Atg	0	0.642	CCCCCCAGCACGGTGCCCGTG
TRIM54	57159	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	27522276	27522276	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28	16			ENST00000296098.4:c.505C>T	p.Arg169Cys	p.R169C	ENST00000296098	NM_032546.3	169	Cgc/Tgc	0	0.522	CATTTACAAACGCCAGAAGGT
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	72	41			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
FLNB	2317	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	58095050	58095050	+	splice_donor_variant	Splice_Site	SNP	G	G	C			TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	13	8			ENST00000490882.1:c.2199+1G>C		p.X733_splice	ENST00000490882	NM_001164317.1			0	0.552	CCCCTACAGGGTAGGTTGTGA
SUMF2	25870	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	56145816	56145816	+	stop_gained	Nonsense_Mutation	SNP	A	A	T			TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	156	17			ENST00000342190.6:c.670A>T	p.Lys224Ter	p.K224*	ENST00000342190	NM_001130069.2	224	Aaa/Taa	0	0.532	CAAGGGAGACAAAGCTGAGGA
KLHL15	80311	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	24006740	24006740	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	135	103			ENST00000328046.8:c.1113A>G	p.Glu371=	p.E371=	ENST00000328046	NM_030624.2	371	gaA/gaG	0	0.458	CTACAGCAAATTCAGAGCGTG
SOX3	6658	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	139586763	139586763	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	43	39			ENST00000370536.2:c.463C>T	p.Arg155Cys	p.R155C	ENST00000370536	NM_005634.2	155	Cgc/Tgc	0	0.632	GCCATTTTGCGCCGCTGCCCG
FLNA	2316	hgsc.bcm.edu;broad.mit.edu	GRCh37	X	153593776	153593776	+	missense_variant	Missense_Mutation	SNP	A	A	T			TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	103	9			ENST00000369850.3:c.1508T>A	p.Phe503Tyr	p.F503Y	ENST00000369850	NM_001110556.1	503	tTc/tAc	0	0.672	GTACACCTTGAAGTCAGCTGT
APOB	338	broad.mit.edu;ucsc.edu	GRCh37	2	21227213	21227213	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40	38			ENST00000233242.1:c.12015C>T	p.Ala4005=	p.A4005=	ENST00000233242	NM_000384.2	4005	gcC/gcT	0	0.507	CGGTGCCTACGGCTGGGGAGG
KRT16P2	400578	broad.mit.edu;ucsc.edu	GRCh37	17	16734855	16734855	+	non_coding_transcript_exon_variant,non_coding_transcript_variant	RNA	SNP	C	C	T	rs688852	by1000genomes	TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	53	6			ENST00000399048.2:n.720G>A		*240*	ENST00000399048				0	0.632	CACAGTCTGCCGCAGGGCCAG
MYH2	4620	broad.mit.edu;ucsc.edu	GRCh37	17	10432336	10432336	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74	33			ENST00000245503.5:c.3415G>A	p.Glu1139Lys	p.E1139K	ENST00000245503	NM_017534.5	1139	Gag/Aag	0	0.582	CGCTGCTTCTCTGCTTTGGCC
ZNF292	23036	broad.mit.edu;hgsc.bcm.edu	GRCh37	6	87966376	87966377	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-			TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28	11			ENST00000369577.3:c.3032_3033delTC	p.Leu1011GlnfsTer4	p.L1011Qfs*4	ENST00000369577	NM_015021.1	1010	aCT/a	0	0.356	AATTCAGAAACTCTCAAAATAG
SPDYE1	285955	broad.mit.edu;hgsc.bcm.edu	GRCh37	7	44042300	44042301	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-			TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	50	19			ENST00000258704.3:c.371_372delCT	p.Pro124ArgfsTer3	p.P124Rfs*3	ENST00000258704	NM_175064.2	124	cCT/c	0	0.614	GTGCTCGCCCCTGAGCCTGAGG
GNAI1	2770	broad.mit.edu;hgsc.bcm.edu	GRCh37	7	79846804	79846805	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-			TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28	13			ENST00000351004.3:c.1062_1063delTT	p.Phe354LeufsTer15	p.F354Lfs*15	ENST00000351004	NM_002069.5	354	TTt/t	0	0.342	TTGTGGTCTCTTTTAAGTTTTG
NOTCH1	4851	broad.mit.edu;hgsc.bcm.edu	GRCh37	9	139413070	139413072	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-			TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	20	10			ENST00000277541.6:c.1070_1072delTCT	p.Phe357del	p.F357del	ENST00000277541	NM_017617.3	357	tTCTac/tac	0	0.655	CACTCGCAGTAGAAGGAGGCCAC
ANO9	338440	broad.mit.edu;hgsc.bcm.edu	GRCh37	11	418481	418483	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-			TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	105	51			ENST00000332826.6:c.2237_2239delAGA	p.Lys746del	p.K746del	ENST00000332826	NM_001012302.2	746	aAGAtg/atg	0	0.621	CCATGCCACATCTTCTCACGCAG
CLUH	23277	broad.mit.edu;hgsc.bcm.edu	GRCh37	17	2601759	2601761	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-			TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	48	11			ENST00000570628.2:c.1276_1278delTTC	p.Phe426del	p.F426del	ENST00000570628		426	TTC/-	0	0.611	AGCCCAGGCTGAAGAAGATGTTG
CIC	23152	broad.mit.edu;hgsc.bcm.edu	GRCh37	19	42798099	42798100	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-			TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73	64			ENST00000575354.2:c.4054_4055delGA	p.Glu1352SerfsTer9	p.E1352Sfs*9	ENST00000575354	NM_015125.3	1351	tcAGaa/tcaa	0	0.678	GGGTCCTGTCAGAAGTGGACTT
NKX2-2	4821	broad.mit.edu;hgsc.bcm.edu	GRCh37	20	21492574	21492574	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-			TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36	34			ENST00000377142.4:c.809delA	p.Gln270ArgfsTer47	p.Q270Rfs*47	ENST00000377142	NM_002509.3	270	cAg/cg	0	0.706	CCAAGTCCACTGCTGGGCCTG
BCOR	54880	broad.mit.edu;hgsc.bcm.edu	GRCh37	X	39932365	39932366	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-			TCGA-DU-7302-01	TCGA-DU-7302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	131	53			ENST00000378444.4:c.2233_2234delAG	p.Arg745GlufsTer6	p.R745Efs*6	ENST00000378444	NM_001123385.1	745	AGg/g	0	0.515	CCGGGATCTCCTCTCTGGTTTC
FERMT3	83706	hgsc.bcm.edu;broad.mit.edu	GRCh37	11	63988497	63988497	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-FG-8182-01	TCGA-FG-8182-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	128	8			ENST00000279227.5:c.1567C>T	p.Arg523Trp	p.R523W	ENST00000279227	NM_178443.2	523	Cgg/Tgg	0	0.652	GCTCACCCCACGGATCCTGGA
EXPH5	23086	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	108381318	108381318	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-FG-8182-01	TCGA-FG-8182-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47	56			ENST00000265843.4:c.4916G>A	p.Cys1639Tyr	p.C1639Y	ENST00000265843	NM_015065.2	1639	tGc/tAc	0	0.483	CAGTGGGTTGCACTCCACTGT
LRIG3	121227	hgsc.bcm.edu;broad.mit.edu	GRCh37	12	59276787	59276787	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-FG-8182-01	TCGA-FG-8182-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	70	4			ENST00000320743.3:c.1344C>T	p.Cys448=	p.C448=	ENST00000320743	NM_153377.4	448	tgC/tgT	0	0.403	GCTGGCAATCGCACAAAAGGC
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252		TCGA-FG-8182-01	TCGA-FG-8182-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	55	12			ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	0	0.537	CGGAACATCTCGAAGCGCTCA
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs68140816		TCGA-FG-8182-01	TCGA-FG-8182-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67	56			ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2			0	0.532	GGGCAACTGACCGTGCAAGTC
CWC25	54883	hgsc.bcm.edu;broad.mit.edu	GRCh37	17	36958970	36958970	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-FG-8182-01	TCGA-FG-8182-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	114	9			ENST00000225428.5:c.1146G>A	p.Arg382=	p.R382=	ENST00000225428	NM_017748.4	382	cgG/cgA	0	0.547	ACTTCCCATCCCGGGAGTCCA
ERCC1	2067	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	45916941	45916941	+	synonymous_variant	Silent	SNP	A	A	T			TCGA-FG-8182-01	TCGA-FG-8182-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	131	13			ENST00000013807.5:c.837T>A	p.Pro279=	p.P279=	ENST00000013807	NM_202001.2	279	ccT/ccA	0	0.522	TTACTTTCTGAGGGCCCAGGC
DNAJC6	9829	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	65858364	65858364	+	synonymous_variant	Silent	SNP	T	T	G			TCGA-FG-8182-01	TCGA-FG-8182-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	56	7			ENST00000371069.4:c.1719T>G	p.Ala573=	p.A573=	ENST00000371069	NM_001256864.1	573	gcT/gcG	0	0.582	CGCCAGCGGCTCCTCCCACCA
C20orf26	26074	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	20	20123549	20123549	+	missense_variant	Missense_Mutation	SNP	A	A	T			TCGA-FG-8182-01	TCGA-FG-8182-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	19	6			ENST00000245957.5:c.908A>T	p.Glu303Val	p.E303V	ENST00000245957	NM_015585.3	303	gAg/gTg	0	0.488	ATAGTCGAGGAGTTGCAGGAA
ADSL	158	hgsc.bcm.edu;broad.mit.edu	GRCh37	22	40762494	40762494	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-FG-8182-01	TCGA-FG-8182-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	55	5			ENST00000216194.7:c.1423G>A	p.Val475Met	p.V475M	ENST00000216194	NM_000026.2	475	Gtg/Atg	0	0.358	ATATGAAAGCGTGATGAAGGT
MYO3B	140469	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	171509614	171509614	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-FG-8182-01	TCGA-FG-8182-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71	8			ENST00000408978.4:c.4009T>C	p.Ser1337Pro	p.S1337P	ENST00000408978	NM_138995.4	1337	Tct/Cct	0	0.418	AAAAGGAGACTCTTTTGCTCA
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-FG-8182-01	TCGA-FG-8182-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64	34			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
RPL37A	6168	hgsc.bcm.edu;broad.mit.edu	GRCh37	2	217364056	217364056	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-FG-8182-01	TCGA-FG-8182-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	86	8			ENST00000491306.1:c.67C>T	p.Arg23Trp	p.R23W	ENST00000491306	NM_000998.4	23	Cgg/Tgg	0	0.502	GGCCTCCCTCCGGAAAATGGT
COL6A3	1293	hgsc.bcm.edu;broad.mit.edu	GRCh37	2	238277572	238277572	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-FG-8182-01	TCGA-FG-8182-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	59	5			ENST00000295550.4:c.4534T>C	p.Ser1512Pro	p.S1512P	ENST00000295550	NM_004369.3	1512	Tcc/Ccc	0	0.562	TTCAGTGGGGACCCCCCTCTG
BRD8	10902	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	137501597	137501597	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-FG-8182-01	TCGA-FG-8182-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	60	9			ENST00000254900.5:c.1198A>G	p.Met400Val	p.M400V	ENST00000254900	NM_139199.1	400	Atg/Gtg	0	0.458	GCAATATCCATCTTCTCAGCC
CD109	135228	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	74491008	74491008	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-FG-8182-01	TCGA-FG-8182-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	46	6			ENST00000287097.5:c.1929T>C	p.Asp643=	p.D643=	ENST00000287097		643	gaT/gaC	0	0.323	TATTGACAGATGCAAACCTCA
MDN1	23195	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	90397120	90397120	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-FG-8182-01	TCGA-FG-8182-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	66	13			ENST00000369393.3:c.11393G>A	p.Arg3798Gln	p.R3798Q	ENST00000369393		3798	cGg/cAg	0	0.403	AAGATGTTTCCGCAAAGACAA
FBXL18	80028	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	5540405	5540405	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-FG-8182-01	TCGA-FG-8182-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88	19			ENST00000382368.3:c.1495A>G	p.Met499Val	p.M499V	ENST00000382368	NM_024963.4	499	Atg/Gtg	0	0.672	TTGCGGGGCATGGCGGAGGAG
CNTLN	54875	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	17236520	17236520	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-FG-8182-01	TCGA-FG-8182-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	49	11			ENST00000380647.3:c.783G>A	p.Leu261=	p.L261=	ENST00000380647		261	ctG/ctA	0	0.368	TAAATGACCTGGAGAAATTGA
VSIG4	11326	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	65253475	65253475	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-FG-8182-01	TCGA-FG-8182-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75	19			ENST00000374737.4:c.253C>T	p.Arg85Cys	p.R85C	ENST00000374737	NM_001257403.1	85	Cgc/Tgc	0	0.547	ACATGCAGGCGGCCCTGGTAC
UNC93A	54346	broad.mit.edu;ucsc.edu	GRCh37	6	167728856	167728856	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-FG-8182-01	TCGA-FG-8182-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	360	30			ENST00000230256.3:c.1290C>T	p.Cys430=	p.C430=	ENST00000230256	NM_018974.3	430	tgC/tgT	0	0.542	TTGTGGAGTGCGTGGAGTCCA
IGFBP2	3485	broad.mit.edu;ucsc.edu	GRCh37	2	217525369	217525369	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-FG-8182-01	TCGA-FG-8182-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	63	11			ENST00000233809.4:c.532C>T	p.Arg178Trp	p.R178W	ENST00000233809	NM_000597.2	178	Cgg/Tgg	0	0.612	CAGTGCTGGCCGGAAGCCCCT
HIVEP2	3097	broad.mit.edu;ucsc.edu	GRCh37	6	143095693	143095693	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-FG-8182-01	TCGA-FG-8182-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	207	29			ENST00000367603.2:c.183A>G	p.Ala61=	p.A61=	ENST00000367603	NM_006734.3	61	gcA/gcG	0	0.498	CAAACAGTTGTGCTGATGCTG
FLRT2	23768	broad.mit.edu;ucsc.edu	GRCh37	14	86089274	86089274	+	synonymous_variant	Silent	SNP	C	C	T	rs146568257	byFrequency	TCGA-FG-8182-01	TCGA-FG-8182-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	96	45			ENST00000330753.4:c.1416C>T	p.Ser472=	p.S472=	ENST00000330753	NM_013231.4	472	agC/agT	0	0.517	GCATAGTCAGCGGTGAGAAGC
MUC16	94025	broad.mit.edu;ucsc.edu	GRCh37	19	8987333	8987333	+	splice_region_variant,synonymous_variant	Splice_Region	SNP	G	G	A			TCGA-FG-8182-01	TCGA-FG-8182-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	112	14			ENST00000397910.4:c.41754C>T	p.Thr13918=	p.T13918=	ENST00000397910	NM_024690.2	13918	acC/acT	0	0.597	TGACCACCCCGGCTAGGGCAG
TNFRSF9	3604	broad.mit.edu;ucsc.edu	GRCh37	1	7998823	7998823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs9657963	byFrequency	TCGA-FG-8182-01	TCGA-FG-8182-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	157	17			ENST00000377507.3:c.166G>A	p.Ala56Thr	p.A56T	ENST00000377507	NM_001561.5	56	Gca/Aca	0	0.408	TGTCCACCTGCGCTGGAGAAA
ADAMTS9	56999	broad.mit.edu;ucsc.edu	GRCh37	3	64526873	64526873	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-FG-8182-01	TCGA-FG-8182-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	120	23			ENST00000498707.1:c.5419G>A	p.Gly1807Arg	p.G1807R	ENST00000498707	NM_182920.1	1807	Ggg/Agg	0	0.473	CGCCGGCTCCCGTTATAGGGA
ATRX	546	broad.mit.edu;hgsc.bcm.edu	GRCh37	X	76890105	76890106	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CATA			TCGA-FG-8182-01	TCGA-FG-8182-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61	16			ENST00000373344.5:c.4785_4788dupTATG	p.Gly1597TyrfsTer5	p.G1597Yfs*5	ENST00000373344	NM_000489.3	1596	-/TATG	0	0.371	TTACCAAGGCCCATACAGTGGG
TCF12	6938	broad.mit.edu	GRCh37	15	57565437	57565438	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TTGAC			TCGA-FG-8182-01	TCGA-FG-8182-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	51	9			ENST00000438423.2:c.1956_1957insTGACT	p.Ser653Ter	p.S653*	ENST00000438423	NM_207037.1	652	ctt/ctTTGACt	0	0.441	GCAGTCATCCTTAGTCTAGAAC
ATRX	546	broad.mit.edu	GRCh37	X	76938654	76938655	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T			TCGA-FG-8182-01	TCGA-FG-8182-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64	9			ENST00000373344.5:c.2093dupA	p.Asp699GlyfsTer2	p.D699Gfs*2	ENST00000373344	NM_000489.3	698	aag/aaAg	0	0.356	TACGCTTATCCTTTTTTCTCAC
ATRX	546	broad.mit.edu	GRCh37	X	76845302	76845302	+	splice_donor_variant	Splice_Site	SNP	A	A	G			TCGA-FG-8182-01	TCGA-FG-8182-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8	3			ENST00000373344.5:c.6217+2T>C		p.X2073_splice	ENST00000373344	NM_000489.3			0	0.328	TTTGTAGCTCACCTTTATAAA
SLIT1	6585	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	98797514	98797514	+	synonymous_variant	Silent	SNP	G	G	A	rs141130521	byFrequency	TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29	23			ENST00000266058.4:c.2307C>T	p.Asp769=	p.D769=	ENST00000266058	NM_003061.2	769	gaC/gaT	0	0.597	ACTGGTTCCCGTCCAAATAGC
MS4A12	54860	hgsc.bcm.edu;broad.mit.edu	GRCh37	11	60268575	60268575	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	181	11			ENST00000016913.4:c.334A>G	p.Ile112Val	p.I112V	ENST00000016913	NM_017716.2	112	Ata/Gta	0	0.373	TTTGTGTTTAATATCCTTCTC
C11orf82	220042	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	82643883	82643883	+	synonymous_variant	Silent	SNP	A	A	T			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24	17			ENST00000533655.1:c.1503A>T	p.Gly501=	p.G501=	ENST00000533655	NM_145018.3	501	ggA/ggT	0	0.368	ACTGTAAAGGAAATCTAAGTC
KDM4E	390245	hgsc.bcm.edu;broad.mit.edu	GRCh37	11	94759050	94759050	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9	11			ENST00000450979.2:c.329C>T	p.Pro110Leu	p.P110L	ENST00000450979	NM_001161630.1	110	cCg/cTg	0	0.468	TATCAGACTCCGCCACACCAG
RASSF9	9182	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	86199470	86199470	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	141	14			ENST00000361228.3:c.318G>A	p.Glu106=	p.E106=	ENST00000361228	NM_005447.3	106	gaG/gaA	0	0.448	TATTGGGCTGCTCATCTCCCC
UHRF1BP1L	23074	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	100478361	100478361	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	59	29			ENST00000279907.7:c.1181A>G	p.His394Arg	p.H394R	ENST00000279907	NM_015054.1	394	cAt/cGt	0	0.393	CTCAAATTCATGCAATAACTC
BAHD1	22893	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	40751367	40751367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150307966		TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42	29			ENST00000416165.1:c.704G>A	p.Arg235His	p.R235H	ENST00000416165	NM_014952.3	235	cGc/cAc	0	0.627	GTAGATGGGCGCTCCACTGAG
CA5A	763	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	87938397	87938397	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	114	44			ENST00000309893.2:c.454G>A	p.Ala152Thr	p.A152T	ENST00000309893	NM_001739.1	152	Gca/Aca	0	0.577	CAAACCTCTGCGGGGTACGCG
KSR1	8844	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	25932772	25932772	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	26	19			ENST00000398988.3:c.1582C>T	p.Arg528Trp	p.R528W	ENST00000398988	NM_014238.1	528	Cgg/Tgg	0	0.597	CCGGCAGACGCGGCATGAGAA
UNC13A	23025	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	17752258	17752258	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	53	31			ENST00000519716.2:c.2580G>T	p.Glu860Asp	p.E860D	ENST00000519716	NM_001080421.2	860	gaG/gaT	0	0.567	CGTCCACAATCTCCTGGGCTG
ZNF614	80110	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	52519785	52519785	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	72	11			ENST00000270649.6:c.1066C>T	p.Arg356Cys	p.R356C	ENST00000270649	NM_025040.3	356	Cgc/Tgc	0	0.428	ACAAGATAGCGCTTCATGGTG
LRRC8B	23507	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	90049110	90049110	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	34	52			ENST00000330947.2:c.901C>T	p.Arg301Cys	p.R301C	ENST00000330947	NM_001134476.1	301	Cgc/Tgc	0	0.383	AGGATATAAGCGCTACCAGTG
MAVS	57506	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	20	3841977	3841977	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93	51			ENST00000428216.2:c.293-2A>G		p.X98_splice	ENST00000428216	NM_020746.4			0	0.602	TTTGTCCTCTAGGGACCTCGG
ADAMTS1	9510	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	21	28210518	28210518	+	missense_variant	Missense_Mutation	SNP	T	T	A			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28	27			ENST00000284984.3:c.2284A>T	p.Arg762Trp	p.R762W	ENST00000284984	NM_006988.3	762	Agg/Tgg	0	0.448	CCATTGTTCCTGGATCCCCTC
ERG	2078	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	21	39774503	39774503	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	38	15			ENST00000288319.7:c.649C>T	p.Arg217Trp	p.R217W	ENST00000288319	NM_182918.3	217	Cgg/Tgg	0	0.438	TGCATTAACCGTGGAGAGTTT
ZNF280A	129025	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	22	22869694	22869694	+	synonymous_variant	Silent	SNP	C	C	T	rs150360634		TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	114	67			ENST00000302097.3:c.261G>A	p.Ser87=	p.S87=	ENST00000302097	NM_080740.3	87	tcG/tcA	0	0.468	TTGCAGGCTGCGACACGTGAG
SCN2A	6326	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	166245292	166245292	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	98	53			ENST00000357398.3:c.4976C>A	p.Ala1659Glu	p.A1659E	ENST00000357398		1659	gCg/gAg	0	0.493	TCCCTTCCTGCGTTGTTTAAC
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	52	41			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
SLC36A1	206358	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	150867793	150867793	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs140057648		TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45	29			ENST00000243389.3:c.1409A>G	p.Asn470Ser	p.N470S	ENST00000243389	NM_078483.2	470	aAt/aGt	0	0.567	ATCTTCATCAATTCCACCTGT
SLIT3	6586	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	168093480	168093480	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23	12			ENST00000519560.1:c.4551C>T	p.Cys1517=	p.C1517=	ENST00000519560	NM_003062.3	1517	tgC/tgT	0	0.627	CGAGGCAGCCGCACTCTAAGT
KLHDC10	23008	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	129761996	129761996	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	56	66			ENST00000335420.5:c.733A>G	p.Thr245Ala	p.T245A	ENST00000335420	NM_014997.3	245	Aca/Gca	0	0.423	CAGAGAGTGGACACAACTGAA
CDCA2	157313	hgsc.bcm.edu;ucsc.edu	GRCh37	8	25337481	25337481	+	synonymous_variant	Silent	SNP	G	G	A	rs112148375	byFrequency	TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	69	32			ENST00000330560.3:c.873G>A	p.Ser291=	p.S291=	ENST00000330560	NM_152562.2	291	tcG/tcA	0	0.507	ATGCCGTTTCGCCTGACACGT
CCDC88B	283234	broad.mit.edu;ucsc.edu	GRCh37	11	64111866	64111866	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs142814776		TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	44	19			ENST00000356786.5:c.1853A>C	p.Gln618Pro	p.Q618P	ENST00000356786	NM_032251.5	618	cAg/cCg	0	0.647	CAGGCCCCGCAGTTGCTGGGA
SZT2	23334	broad.mit.edu;hgsc.bcm.edu	GRCh37	1	43912030	43912033	+	frameshift_variant	Frame_Shift_Del	DEL	CAAA	CAAA	-			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24	36			ENST00000562955.1:c.8846_8849delAACA	p.Lys2949SerfsTer33	p.K2949Sfs*33	ENST00000562955	NM_015284.3	2948	gtCAAA/gt	0	0.559	ACTTCTGTGTCAAACAGTTTGCCC
PI4KB	5298	broad.mit.edu;hgsc.bcm.edu	GRCh37	1	151265460	151265461	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	55	46			ENST00000368875.2:c.2354_2355delAA	p.Lys785ArgfsTer9	p.K785Rfs*9	ENST00000368875	NM_002651.2	785	aAA/a	0	0.564	GGAACCTCTCTTTGAGGTTTCG
OR14A16	284532	broad.mit.edu;hgsc.bcm.edu	GRCh37	1	247978839	247978840	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	44	29			ENST00000357627.1:c.192_193delAT	p.Ser65PhefsTer54	p.S65Ffs*54	ENST00000357627	NM_001001966.1	64	ctATct/ctct	0	0.421	TCCAAGAAAGATAGATTCTTCA
BRE	9577	broad.mit.edu;hgsc.bcm.edu	GRCh37	2	28550157	28550158	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	135	57			ENST00000344773.2:c.1108_1109delGA	p.Asp370CysfsTer152	p.D370Cfs*152	ENST00000344773	NM_004899.4	369	AGa/a	0	0.609	CCAAGGGAGCAGAGATGCCTGC
RAB3GAP1	22930	broad.mit.edu;hgsc.bcm.edu	GRCh37	2	135920344	135920346	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	75	29			ENST00000442034.1:c.2417_2419delAGA	p.Lys806del	p.K806del	ENST00000442034	NM_001172435.1	805	AAG/-	0	0.315	TTCTTCAGTTAAGAAGATCATAA
SP3	6670	broad.mit.edu;hgsc.bcm.edu	GRCh37	2	174774916	174774917	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	53	42			ENST00000310015.6:c.2098_2099delAT	p.Ile700Ter	p.I700*	ENST00000310015	NM_001172712.1	700	ATt/t	0	0.376	GTGTGTTTTAATATGTTTGGCA
ZBTB20	26137	broad.mit.edu;hgsc.bcm.edu	GRCh37	3	114058229	114058231	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	51	26			ENST00000474710.1:c.1847_1849delCCT	p.Ser616del	p.S616del	ENST00000474710	NM_001164342.1	616	tCCTta/tta	0	0.507	TAATCCTTTAAGGAGAAGGAGCG
GALNTL6	442117	broad.mit.edu;hgsc.bcm.edu	GRCh37	4	173961139	173961141	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	60	25			ENST00000506823.1:c.1700_1702delAGA	p.Lys567del	p.K567del	ENST00000506823	NM_001034845.2	565	gAGAag/gag	0	0.424	AACCCCGCAGAGAAGAAGATTTT
FNDC9	408263	broad.mit.edu;hgsc.bcm.edu	GRCh37	5	156770389	156770391	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	89	47			ENST00000312349.4:c.154_156delGAG	p.Glu52del	p.E52del	ENST00000312349	NM_001001343.3	52	GAG/-	0	0.537	GAGGCACCTTCTCCTCGTGGTGG
EPB41L2	2037	broad.mit.edu;hgsc.bcm.edu	GRCh37	6	131277495	131277497	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	85	36			ENST00000337057.3:c.129_131delGGA	p.Glu44del	p.E44del	ENST00000337057	NM_001431.3	43	gaGGAa/gaa	0	0.483	GGAACCTTTTTCCTCCTCTGGAT
KMT2E	55904	broad.mit.edu;hgsc.bcm.edu	GRCh37	7	104717788	104717789	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37	41			ENST00000311117.3:c.1040_1041delAA	p.Lys347ArgfsTer5	p.K347Rfs*5	ENST00000311117	NM_182931.2	346	gcAAaa/gcaa	0	0.292	TTAAATCTGCAAAAGATTTGCC
FAM91A1	157769	broad.mit.edu;hgsc.bcm.edu	GRCh37	8	124789562	124789563	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TG	TG	-			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	53	17			ENST00000334705.7:c.367+1_367+2delGT		p.X123_splice	ENST00000334705	NM_144963.2	123		0	0.302	TGCTGCTGACTGTAAGTATTTA
RUSC2	9853	broad.mit.edu;hgsc.bcm.edu	GRCh37	9	35560631	35560633	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	15	10			ENST00000455600.1:c.3998_4000delAGG	p.Glu1333del	p.E1333del	ENST00000455600	NM_001135999.1	1332	GAG/-	0	0.7	CCCTGCCTCTGAGGAGGCCCTGG
ARHGEF39	84904	broad.mit.edu;hgsc.bcm.edu	GRCh37	9	35663036	35663037	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	70	51			ENST00000378387.3:c.579_580delAG	p.Arg193SerfsTer11	p.R193Sfs*11	ENST00000378387	NM_032818.2	193	agAGtc/agtc	0	0.53	ATAGTATGGACTCTCTGGGCAG
NOTCH1	4851	broad.mit.edu;hgsc.bcm.edu	GRCh37	9	139397632	139397635	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ACTC	ACTC	-			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	71	19			ENST00000277541.6:c.5166_5167+2delGAGT		p.X1722_splice	ENST00000277541	NM_017617.3	1722		0	0.662	GGCCACACTTACTCTGCACGGCCT
NOTCH1	4851	broad.mit.edu;hgsc.bcm.edu	GRCh37	9	139413073	139413075	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	25	24			ENST00000277541.6:c.1067_1069delCCT	p.Ser356del	p.S356del	ENST00000277541	NM_017617.3	356	tCCTtc/ttc	0	0.65	TCGCAGTAGAAGGAGGCCACACG
KAT6B	23522	broad.mit.edu;hgsc.bcm.edu	GRCh37	10	76784946	76784949	+	frameshift_variant	Frame_Shift_Del	DEL	ACAA	ACAA	-			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	59	23			ENST00000287239.4:c.3606_3609delAACA	p.Thr1203ArgfsTer21	p.T1203Rfs*21	ENST00000287239	NM_001256468.1	1201	agACAA/ag	0	0.451	GGAAGAAAAGACAAACAGAGGAAG
CLEC9A	283420	broad.mit.edu;hgsc.bcm.edu	GRCh37	12	10205309	10205321	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCTCTTCAGTG	CCTCTCTTCAGTG	-			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	54	11			ENST00000355819.1:c.23_35delCCTCTCTTCAGTG	p.Thr8ArgfsTer25	p.T8Rfs*25	ENST00000355819	NM_207345.2	8	aCCTCTCTTCAGTGg/ag	0	0.441	GAAATATACACCTCTCTTCAGTGGGATAGCCCA
ALDH1L2	160428	broad.mit.edu;hgsc.bcm.edu	GRCh37	12	105464505	105464507	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	85	20			ENST00000258494.9:c.269_271delAAG	p.Glu90del	p.E90del	ENST00000258494	NM_001034173.3	90	gAAGtg/gtg	0	0.463	GCTTCTGCCACTTCTTTGATGGT
BRMS1L	84312	broad.mit.edu;hgsc.bcm.edu	GRCh37	14	36295747	36295749	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9	11			ENST00000216807.7:c.28_30delAAG	p.Lys10del	p.K10del	ENST00000216807	NM_032352.3	9	AAG/-	0	0.631	CCGAGGGGATAAGAAGGAGACCA
PIGW	284098	broad.mit.edu;hgsc.bcm.edu	GRCh37	17	34893506	34893508	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	141	50			ENST00000592983.1:c.561_563delGAG	p.Arg188del	p.R188del	ENST00000592983		186	AGG/-	0	0.424	TCTAGAGGTCAGGAGGAGAAAAT
SPECC1L	23384	broad.mit.edu;hgsc.bcm.edu	GRCh37	22	24718811	24718812	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	101	50			ENST00000314328.9:c.1864_1865delTT	p.Leu622GlyfsTer2	p.L622Gfs*2	ENST00000314328	NM_015330.4	621	acTTtg/actg	0	0.416	AAGCAGAGACTTTGGCTAGTAG
BCOR	54880	broad.mit.edu	GRCh37	X	39934072	39934075	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-			TCGA-HW-A5KJ-01	TCGA-HW-A5KJ-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	80	7			ENST00000378444.4:c.524_527delAACA	p.Lys175ArgfsTer40	p.K175Rfs*40	ENST00000378444	NM_001123385.1	175	aAACAg/ag	0	0.539	GAGAGGGCTCTGTTTGTCGCTGGC
OR4A15	81328	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	55136122	55136122	+	missense_variant	Missense_Mutation	SNP	A	A	T			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	78	64			ENST00000314706.3:c.763A>T	p.Thr255Ser	p.T255S	ENST00000314706	NM_001005275.1	255	Act/Tct	0	0.438	CTCTCTTAAGACTCAGAGTTT
OR5D16	390144	hgsc.bcm.edu;broad.mit.edu	GRCh37	11	55606760	55606760	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	55	5			ENST00000378396.1:c.533A>G	p.His178Arg	p.H178R	ENST00000378396	NM_001005496.1	178	cAt/cGt	0	0.423	ACAATCAATCATTTCTTCTGT
NPAS4	266743	hgsc.bcm.edu;broad.mit.edu	GRCh37	11	66192121	66192121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142965018	byFrequency	TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	183	17			ENST00000311034.2:c.1760C>T	p.Thr587Met	p.T587M	ENST00000311034	NM_178864.3	587	aCg/aTg	0	0.607	GGGGACTGCACGCTCTTGGCC
MMP1	4312	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	102666337	102666337	+	splice_region_variant,synonymous_variant	Splice_Region	SNP	C	C	T			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29	11			ENST00000315274.6:c.627G>A	p.Glu209=	p.E209=	ENST00000315274	NM_002421.3	209	gaG/gaA	0	0.368	GTAAGTTGTACTCTAAAAAGG
GRIN2B	2904	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	13716801	13716801	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29	20			ENST00000609686.1:c.3371G>A	p.Arg1124Lys	p.R1124K	ENST00000609686	NM_000834.3	1124	aGg/aAg	0	0.617	TTCCTTGTCCCTGAAGTAGCG
KRT84	3890	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	52777394	52777394	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	18	18			ENST00000257951.3:c.735C>T	p.Val245=	p.V245=	ENST00000257951	NM_033045.3	245	gtC/gtT	0	0.577	AGCCCTCTAGGACATCCTGCA
ACAD10	80724	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	112193513	112193513	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	130	19			ENST00000455480.2:c.3096G>A	p.Pro1032=	p.P1032=	ENST00000455480	NM_001136538.1	1032	ccG/ccA	0	0.517	TGGTCGCCCCGTCCATGGCCT
RAB27A	5873	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	55497820	55497820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141362723	by1000genomes	TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84	65			ENST00000396307.2:c.551G>A	p.Arg184Gln	p.R184Q	ENST00000396307	NM_004580.4	184	cGa/cAa	0	0.463	CCGTTCCATTCGCTTCATTAT
HSDL1	83693	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	84163854	84163854	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	165	16			ENST00000219439.4:c.403C>T	p.Pro135Ser	p.P135S	ENST00000219439	NM_001146051.1	135	Cca/Tca	0	0.473	TCTCGAATTGGAAGGTAGATC
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	by1000genomes	TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3	29			ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	0	0.542	GGCACAAACACGCACCTCAAA
ARHGEF10L	55160	hgsc.bcm.edu;broad.mit.edu	GRCh37	1	17961457	17961457	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	46	3			ENST00000361221.3:c.1873G>C	p.Val625Leu	p.V625L	ENST00000361221	NM_018125.3	625	Gtg/Ctg	0	0.642	CAAGGACAATGTGCTCATCCA
ELMOD3	84173	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	85617291	85617291	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	46	23			ENST00000315658.7:c.846C>T	p.Pro282=	p.P282=	ENST00000315658	NM_032213.4	282	ccC/ccT	0	0.567	AGGTCATCCCCGTGGTGAACA
GPR39	2863	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	133175296	133175296	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	50	30			ENST00000329321.3:c.681C>T	p.Ala227=	p.A227=	ENST00000329321	NM_001508.2	227	gcC/gcT	0	0.612	TCTTCGGCGCCTTCGTGGTCT
TANK	10010	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	162087893	162087893	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	126	10			ENST00000392749.2:c.932C>T	p.Pro311Leu	p.P311L	ENST00000392749	NM_001199135.1	311	cCc/cTc	0	0.383	AAAACAAAGCCCTCAAATCTC
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64	24			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
SLC6A11	6538	hgsc.bcm.edu;broad.mit.edu	GRCh37	3	10885932	10885932	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	44	3			ENST00000254488.2:c.657G>C	p.Glu219Asp	p.E219D	ENST00000254488	NM_014229.1	219	gaG/gaC	0	0.587	ACGGGATCGAGCACATCGGGA
MAN2B2	23324	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	6612960	6612960	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21	15			ENST00000285599.3:c.2518C>T	p.Leu840=	p.L840=	ENST00000285599	NM_015274.1	840	Ctg/Ttg	0	0.627	GAGGAGCGCACTGGCGCTGCA
COL25A1	84570	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	109805344	109805344	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47	25			ENST00000399132.1:c.1010C>T	p.Pro337Leu	p.P337L	ENST00000399132	NM_198721.2	337	cCg/cTg	0	0.413	CTTTATCCCCGGAAGTCCAGG
SCAND3	114821	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	28540794	28540794	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45	9			ENST00000452236.2:c.2872T>C	p.Cys958Arg	p.C958R	ENST00000452236	NM_052923.1	958	Tgt/Cgt	0	0.353	tccaaaccacatttgttaaca
PTCHD4	442213	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	47976601	47976601	+	missense_variant	Missense_Mutation	SNP	A	A	T			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	38	18			ENST00000339488.4:c.676T>A	p.Phe226Ile	p.F226I	ENST00000339488	NM_001013732.3	226	Ttt/Att	0	0.527	GTCTTATGAAAGTCCCTCCAG
CDK14	5218	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	90613505	90613505	+	synonymous_variant	Silent	SNP	T	T	A			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	115	42			ENST00000265741.3:c.936T>A	p.Ala312=	p.A312=	ENST00000265741	NM_012395.2	312	gcT/gcA	0	0.348	AAGGAGTTGCTGCTTTTCCAG
XKR9	389668	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	71646066	71646066	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	50	6			ENST00000408926.3:c.529T>C	p.Trp177Arg	p.W177R	ENST00000408926	NM_001011720.1	177	Tgg/Cgg	0	0.299	TGCTATTTCTTGGTCAACTGT
CDH17	1015	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	95182644	95182644	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	101	64			ENST00000027335.3:c.1047C>T	p.Val349=	p.V349=	ENST00000027335	NM_004063.3	349	gtC/gtT	0	0.438	CATTCTCCTGGACCTCAAATA
FAM78A	286336	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	134136482	134136482	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	48	28			ENST00000372271.3:c.579G>A	p.Leu193=	p.L193=	ENST00000372271	NM_033387.3	193	ctG/ctA	0	0.617	TGGTGGCCACCAGCCAGGTGG
FRMD7	90167	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	131214037	131214037	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	34	85			ENST00000298542.4:c.1047A>G	p.Lys349=	p.K349=	ENST00000298542	NM_194277.2	349	aaA/aaG	0	0.398	ACCTTACTTGTTTTGACACAT
RPS4Y2	140032	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	Y	22930744	22930744	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29	22			ENST00000288666.5:c.414C>A	p.His138Gln	p.H138Q	ENST00000288666	NM_001039567.2	138	caC/caA	0	0.438	GAATTCCACACCTGGTGACTC
PALD1	27143	broad.mit.edu;ucsc.edu	GRCh37	10	72307126	72307126	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58	29			ENST00000263563.6:c.2186C>T	p.Ala729Val	p.A729V	ENST00000263563	NM_014431.2	729	gCg/gTg	0	0.617	GTGGACGCAGCGCTGGACACT
GPX2	2877	broad.mit.edu;ucsc.edu	GRCh37	14	65406296	65406296	+	synonymous_variant	Silent	SNP	C	C	T	rs17885748		TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	105	20			ENST00000389614.5:c.483G>A	p.Pro161=	p.P161=	ENST00000389614	NM_002083.3	161	ccG/ccA	0	0.537	GCTCTCCCTCCGGCCCTATGA
FRY	10129	broad.mit.edu;ucsc.edu	GRCh37	13	32852686	32852686	+	splice_donor_variant	Splice_Site	SNP	G	G	C			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	100	16			ENST00000380250.3:c.8469+1G>C		p.X2823_splice	ENST00000380250	NM_023037.2			0	0.443	CGAAGAAAAGGTAATAAAAGC
OR2M7	391196	broad.mit.edu;ucsc.edu	GRCh37	1	248487368	248487368	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	182	108			ENST00000317965.2:c.503A>G	p.Tyr168Cys	p.Y168C	ENST00000317965	NM_001004691.1	168	tAc/tGc	0	0.448	AGACCCACAGTAGGAGAAGGA
MYO18A	399687	broad.mit.edu;ucsc.edu	GRCh37	17	27430667	27430667	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47	3			ENST00000527372.1:c.3457C>G	p.Leu1153Val	p.L1153V	ENST00000527372	NM_078471.3	1153	Ctg/Gtg	0	0.667	AAGCACTCCAGCAGCTCCTCC
APRT	353	broad.mit.edu;ucsc.edu	GRCh37	16	88876924	88876924	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	22	2			ENST00000378364.3:c.228C>T	p.Ala76=	p.A76=	ENST00000378364	NM_000485.2	76	gcC/gcT	0	0.637	CAAGCTCCTGGGCCAGGGAGG
SDAD1P1	404668	broad.mit.edu;ucsc.edu	GRCh37	8	26237249	26237249	+	non_coding_transcript_exon_variant	RNA	SNP	G	G	A			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45	6			ENST00000519902.1:n.2700C>T		*900*	ENST00000519902				0	0.458	GGGATTTCCCGGGGACAGCGT
PHF23	79142	broad.mit.edu;ucsc.edu	GRCh37	17	7139547	7139547	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	81	41			ENST00000320316.3:c.699A>G	p.Pro233=	p.P233=	ENST00000320316	NM_024297.2	233	ccA/ccG	0	0.552	GCCCAGGAGGTGGGAGTCTAT
RUNX1T1	862	broad.mit.edu;ucsc.edu	GRCh37	8	93026829	93026829	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88	12			ENST00000436581.2:c.479G>A	p.Arg160His	p.R160H	ENST00000436581		160	cGc/cAc	0	0.507	AACGAGGGTGCGAACTCTTTC
ASPM	259266	broad.mit.edu;hgsc.bcm.edu	GRCh37	1	197070598	197070599	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs144088344	by1000genomes	TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	32	12			ENST00000367409.4:c.7782_7783delGA	p.Lys2595SerfsTer6	p.K2595Sfs*6	ENST00000367409	NM_018136.4	2594	caGAaa/caaa	0	0.356	TGAAATACTTTCTGTTTCTTTT
AMOTL2	51421	broad.mit.edu;hgsc.bcm.edu	GRCh37	3	134078153	134078155	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	66	21			ENST00000249883.5:c.2074_2076delACA	p.Thr692del	p.T692del	ENST00000249883	NM_016201.3	692	ACA/-	0	0.596	GGGCGTCTGCTGTTTGTCGCTCA
CYP3A7	1551	broad.mit.edu;hgsc.bcm.edu	GRCh37	7	99312223	99312224	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	89	19			ENST00000336374.2:c.752_753delAA	p.Lys251IlefsTer26	p.K251Ifs*26	ENST00000336374	NM_000765.3	251	aAA/a	0	0.312	GTTTTACAGATTTTGTTAGAAA
RANBP6	26953	broad.mit.edu;hgsc.bcm.edu	GRCh37	9	6013101	6013102	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97	24			ENST00000259569.5:c.2506_2507delCT	p.Leu836AlafsTer3	p.L836Afs*3	ENST00000259569	NM_012416.3	836	CTg/g	0	0.337	CTCATCTTGCAGAGACATCTCA
UHRF2	115426	broad.mit.edu;hgsc.bcm.edu	GRCh37	9	6497275	6497278	+	frameshift_variant	Frame_Shift_Del	DEL	CAGT	CAGT	-			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	40	16			ENST00000276893.5:c.1685_1688delTCAG	p.Val562GlufsTer2	p.V562Efs*2	ENST00000276893	NM_152896.2	561	cCAGTc/cc	0	0.426	GCTGGTAAGCCAGTCAGAGTGATA
AKAP8	10270	broad.mit.edu;hgsc.bcm.edu	GRCh37	19	15471767	15471769	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	21	10			ENST00000269701.2:c.1417_1419delTTC	p.Phe473del	p.F473del	ENST00000269701	NM_005858.3	473	TTC/-	0	0.571	CGATCTTCTTGAAGAAGTGCTCC
LENG9	94059	broad.mit.edu;hgsc.bcm.edu	GRCh37	19	54973460	54973461	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	53	44			ENST00000333834.4:c.1315_1316delCA	p.Gln439ValfsTer58	p.Q439Vfs*58	ENST00000333834	NM_198988.1	439	CAg/g	0	0.644	CCCTGGAGACTGTAGTGTACTC
USP9X	8239	broad.mit.edu;hgsc.bcm.edu	GRCh37	X	41088882	41088884	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	34	15			ENST00000324545.8:c.7285_7287delAGA	p.Arg2429del	p.R2429del	ENST00000324545	NM_001039590.2	2427	gaAAGa/gaa	0	0.404	ATGAACTTGAAAGAAGACCATAT
ATRX	546	broad.mit.edu;hgsc.bcm.edu	GRCh37	X	76918976	76918977	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5	21			ENST00000373344.5:c.4014_4015delTA	p.His1338GlnfsTer11	p.H1338Qfs*11	ENST00000373344	NM_000489.3	1338	caTAgg/cagg	0	0.356	CGCAAAAGCCTATGTCTGTATC
ARID1A	8289	broad.mit.edu	GRCh37	1	27057848	27057848	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-			TCGA-HW-7490-01	TCGA-HW-7490-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	245	25			ENST00000324856.7:c.1558delC	p.Gln520SerfsTer99	p.Q520Sfs*99	ENST00000324856	NM_006015.4	519	tCc/tc	0	0.632	CCTCCATACTCCCAGCAGCCA
OR6Q1	219952	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	57799000	57799000	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HW-7491-01	TCGA-HW-7491-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	65	70			ENST00000302622.3:c.576G>A	p.Ser192=	p.S192=	ENST00000302622	NM_001005186.2	192	tcG/tcA	0	0.498	TAGCCTTGTCGTGCTCAGATG
CMKLR1	1240	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	108685742	108685742	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HW-7491-01	TCGA-HW-7491-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	55	29			ENST00000312143.7:c.998G>A	p.Arg333His	p.R333H	ENST00000312143	NM_001142344.1	333	cGc/cAc	0	0.483	ATTGACCAGGCGAGAGAAGAG
SLITRK6	84189	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	13	86370348	86370348	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-HW-7491-01	TCGA-HW-7491-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	22	80			ENST00000400286.2:c.296A>G	p.Asn99Ser	p.N99S	ENST00000400286	NM_032229.2	99	aAt/aGt	0	0.353	ATCTGCAATATTGTTAAATCC
TRIM9	114088	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	14	51448645	51448645	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-HW-7491-01	TCGA-HW-7491-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	58	43			ENST00000298355.3:c.1780C>G	p.Pro594Ala	p.P594A	ENST00000298355	NM_015163.5	594	Cct/Gct	0	0.517	CCAAAGGCAGGATCAGGGTGG
IDH2	3418	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503		TCGA-HW-7491-01	TCGA-HW-7491-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	32	36			ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	0	0.632	ATGGGCGTGCCTGCCAATGGT
DVL2	1856	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7132713	7132713	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-HW-7491-01	TCGA-HW-7491-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62	41			ENST00000005340.5:c.801A>G	p.Thr267=	p.T267=	ENST00000005340	NM_004422.2	267	acA/acG	0	0.567	TTAGCGTGACTGTGATGATAT
CIC	23152	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	42791757	42791757	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HW-7491-01	TCGA-HW-7491-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	10	37			ENST00000575354.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000575354	NM_015125.3	215	Cgg/Tgg	0	0.612	CAAGCGGCACCGGGCCCTGGT
TTC7A	57217	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	47220609	47220609	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HW-7491-01	TCGA-HW-7491-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	57	50			ENST00000319190.5:c.785G>A	p.Arg262Lys	p.R262K	ENST00000319190	NM_020458.2	262	aGa/aAa	0	0.547	AAGGGCATGAGAGAGCTCCGG
AGPS	8540	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	178386040	178386040	+	missense_variant	Missense_Mutation	SNP	T	T	G			TCGA-HW-7491-01	TCGA-HW-7491-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	81	38			ENST00000264167.4:c.1741T>G	p.Phe581Val	p.F581V	ENST00000264167	NM_003659.3	581	Ttt/Gtt	0	0.383	CTACTTCTATTTTGCCTTTAA
SCN10A	6336	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	38739794	38739794	+	synonymous_variant	Silent	SNP	G	G	A	rs142804903		TCGA-HW-7491-01	TCGA-HW-7491-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	77	78			ENST00000449082.2:c.4917C>T	p.Asp1639=	p.D1639=	ENST00000449082	NM_006514.2	1639	gaC/gaT	0	0.547	TGAACATGTCGTCGATGCCAG
TINAG	27283	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	54191662	54191662	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HW-7491-01	TCGA-HW-7491-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	65	32			ENST00000259782.4:c.572G>A	p.Arg191His	p.R191H	ENST00000259782	NM_014464.3	191	cGc/cAc	0	0.373	TTTAAATTTCGCCTTGGCACT
LAMB4	22798	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	107748127	107748127	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-HW-7491-01	TCGA-HW-7491-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45	31			ENST00000388781.3:c.540C>A	p.Asp180Glu	p.D180E	ENST00000388781	NM_007356.2	180	gaC/gaA	0	0.398	CACAAACAATGTCTCCCACTC
SLC37A3	84255	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	140058508	140058508	+	synonymous_variant	Silent	SNP	G	G	A	rs142313913	byFrequency	TCGA-HW-7491-01	TCGA-HW-7491-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99	63			ENST00000326232.9:c.453C>T	p.Asn151=	p.N151=	ENST00000326232	NM_207113.1	151	aaC/aaT	0	0.512	GCAGCAGGCCGTTCACAATCC
VPS13A	23230	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	79936584	79936584	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HW-7491-01	TCGA-HW-7491-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	37	25			ENST00000360280.3:c.5752G>A	p.Asp1918Asn	p.D1918N	ENST00000360280	NM_033305.2	1918	Gat/Aat	0	0.338	TTTAAGTATGGATTATATCCG
PIK3CA	5290	broad.mit.edu;hgsc.bcm.edu	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-			TCGA-HW-7491-01	TCGA-HW-7491-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	54	44			ENST00000263967.3:c.328_330delGAA	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	0	0.34	AGGCAACCGTGAAGAAAAGATCC
FUT5	2527	broad.mit.edu;hgsc.bcm.edu	GRCh37	19	5867346	5867347	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	rs111394159		TCGA-HW-7491-01	TCGA-HW-7491-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39	25			ENST00000252675.5:c.389_390dupCC	p.Ser131ProfsTer118	p.S131Pfs*118	ENST00000252675		130	-/CC	0	0.663	AGGTTGGCACTGGGGTTGTACA
LDB1	8861	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	103871263	103871263	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	66	43			ENST00000425280.1:c.56C>T	p.Ser19Leu	p.S19L	ENST00000425280	NM_001113407.1	19	tCg/tTg	0	0.547	CTCCTTCGGCGAGTACAGCTT
OOSP2	219990	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	59812148	59812148	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	139	28			ENST00000278855.2:c.248T>C	p.Val83Ala	p.V83A	ENST00000278855	NM_173801.3	83	gTt/gCt	0	0.398	TCCTAGGTAGTTTCTGAGGAA
TMEM109	79073	hgsc.bcm.edu;broad.mit.edu	GRCh37	11	60687346	60687346	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	266	15			ENST00000227525.3:c.181G>C	p.Val61Leu	p.V61L	ENST00000227525	NM_024092.2	61	Gtg/Ctg	0	0.542	AGGTCGATCTGTGCGAGGGAC
ZW10	9183	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	113628513	113628513	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	148	16			ENST00000200135.3:c.796A>G	p.Ile266Val	p.I266V	ENST00000200135	NM_004724.3	266	Ata/Gta	0	0.378	TGGCTTTCTATCACAGCATGA
STAB2	55576	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	104049284	104049284	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	56	60			ENST00000388887.2:c.1659C>T	p.Tyr553=	p.Y553=	ENST00000388887	NM_017564.9	553	taC/taT	0	0.423	GTGGACCATACACCATTTTTG
TDG	6996	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	104374683	104374683	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	246	28			ENST00000392872.3:c.421C>T	p.Pro141Ser	p.P141S	ENST00000392872	NM_003211.4	141	Ccg/Tcg	0	0.363	TGGCATAAACCCGGGACTAAT
HS3ST4	9951	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	26147367	26147367	+	missense_variant	Missense_Mutation	SNP	A	A	T			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	86	21			ENST00000331351.5:c.1169A>T	p.Lys390Ile	p.K390I	ENST00000331351	NM_006040.2	390	aAa/aTa	0	0.517	TATTTCAACAAAACCAAGGGG
APOBR	55911	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	28507468	28507468	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	13	16			ENST00000564831.1:c.1106G>A	p.Gly369Glu	p.G369E	ENST00000564831	NM_018690.3	369	gGg/gAg	0	0.657	GCCTCAGGAGGGGACGAGGCC
CDH19	28513	hgsc.bcm.edu;broad.mit.edu	GRCh37	18	64172539	64172539	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	173	10			ENST00000262150.2:c.1829G>A	p.Gly610Glu	p.G610E	ENST00000262150	NM_021153.3	610	gGg/gAg	0	0.303	AAAAATAAACCCTGATGAAGA
DOHH	83475	hgsc.bcm.edu;broad.mit.edu	GRCh37	19	3492382	3492382	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3	3			ENST00000427575.1:c.467G>A	p.Arg156His	p.R156H	ENST00000427575	NM_001145165.1	156	cGt/cAt	0	0.746	CCCCACGTCACGCTCCTCAGC
C3	718	hgsc.bcm.edu;broad.mit.edu	GRCh37	19	6697496	6697496	+	synonymous_variant	Silent	SNP	G	G	A	rs140780068		TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	128	9			ENST00000245907.6:c.2655C>T	p.Thr885=	p.T885=	ENST00000245907	NM_000064.2	885	acC/acT	0	0.587	GGATGGTTACGGTCTGCTGGT
PLD3	23646	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	40883897	40883897	+	synonymous_variant	Silent	SNP	C	C	G			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	147	23			ENST00000409587.1:c.1290C>G	p.Thr430=	p.T430=	ENST00000409587		430	acC/acG	0	0.647	CTCTAGGAACCTCCAACTGGT
HCN3	57657	hgsc.bcm.edu;broad.mit.edu	GRCh37	1	155257756	155257756	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	114	9			ENST00000368358.3:c.1827G>A	p.Ala609=	p.A609=	ENST00000368358	NM_020897.2	609	gcG/gcA	0	0.627	TGGTACATGCGCCCCTTCAGG
OR1C1	26188	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	247920937	247920937	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	45	54			ENST00000408896.2:c.772G>A	p.Val258Ile	p.V258I	ENST00000408896	NM_012353.2	258	Gtc/Atc	0	0.512	CTGAAATAGACGGCGATGGCT
MICALL1	85377	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	22	38323471	38323471	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	48	44			ENST00000215957.6:c.1519C>T	p.Pro507Ser	p.P507S	ENST00000215957	NM_033386.3	507	Cca/Tca	0	0.677	CACACCATCGCCAGCGCTCAG
CLIP4	79745	hgsc.bcm.edu;broad.mit.edu	GRCh37	2	29356592	29356592	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	127	8			ENST00000320081.5:c.439C>T	p.Arg147Cys	p.R147C	ENST00000320081	NM_024692.4	147	Cgc/Tgc	0	0.368	TTTGCGGAGTCGCTGGACAAA
CAPN13	92291	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	30966407	30966407	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	138	104			ENST00000295055.8:c.1287G>A	p.Ser429=	p.S429=	ENST00000295055	NM_144575.2	429	tcG/tcA	0	0.473	TGTTTCTGAACGAGGAAAAAA
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	103	50			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
GRM7	2917	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	7188209	7188209	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	191	39			ENST00000357716.4:c.590G>A	p.Arg197His	p.R197H	ENST00000357716	NM_000844.3	197	cGc/cAc	0	0.522	TTCTTCTCTCGCGTGGTGCCA
KLHL18	23276	hgsc.bcm.edu;broad.mit.edu	GRCh37	3	47361235	47361235	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	296	16			ENST00000232766.5:c.222C>T	p.Cys74=	p.C74=	ENST00000232766	NM_025010.4	74	tgC/tgT	0	0.493	TGATGGAGTGCAAGCAGGATG
GPR116	221395	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	46826878	46826878	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	215	49			ENST00000283296.7:c.2762G>A	p.Ser921Asn	p.S921N	ENST00000283296	NM_001098518.1	921	aGc/aAc	0	0.448	CATCACTAAGCTCTCTGCAAA
MCM9	254394	hgsc.bcm.edu;broad.mit.edu	GRCh37	6	119245149	119245149	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	369	27			ENST00000316316.6:c.448T>C	p.Cys150Arg	p.C150R	ENST00000316316	NM_017696.2	150	Tgc/Cgc	0	0.458	ACATGCTTGCATTTGTTACAC
SCRN1	9805	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	29963705	29963705	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	158	18			ENST00000434476.2:c.1173C>T	p.Thr391=	p.T391=	ENST00000434476	NM_001145514.1	391	acC/acT	0	0.557	GCTCCAGCATGGTGCTCCTCA
RNF133	168433	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	122338205	122338205	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	393	138			ENST00000340112.2:c.768C>T	p.Cys256=	p.C256=	ENST00000340112	NM_139175.1	256	tgC/tgT	0	0.398	AGCAAATTACGCAGCTATCCC
CEP41	95681	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	130038826	130038826	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	490	46			ENST00000223208.5:c.1028G>A	p.Arg343Gln	p.R343Q	ENST00000223208	NM_018718.2	343	cGa/cAa	0	0.577	CTGAGCGCTTCGGGCACCAGG
FAM154A	158297	hgsc.bcm.edu;broad.mit.edu	GRCh37	9	18928507	18928507	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	154	10			ENST00000380534.4:c.968G>A	p.Arg323Gln	p.R323Q	ENST00000380534	NM_153707.2	323	cGa/cAa	0	0.562	AAGTGCAGGTCGGCAGGACTG
SPATA31E1	286234	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	90501762	90501762	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	203	27			ENST00000325643.5:c.2360G>A	p.Arg787His	p.R787H	ENST00000325643	NM_178828.4	787	cGc/cAc	0	0.577	CCTGTGCGTCGCTCCTGGCTC
ABCA2	20	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	139912486	139912486	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	50	11			ENST00000341511.6:c.2035G>A	p.Asp679Asn	p.D679N	ENST00000341511	NM_212533.2	679	Gat/Aat	0	0.662	TCCACCACATCGTGCCCCACA
NDOR1	27158	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	140110623	140110623	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	141	20			ENST00000371521.4:c.1659A>G	p.Ala553=	p.A553=	ENST00000371521	NM_001144026.1	553	gcA/gcG	0	0.642	GCCAGGGTGCATACTTCTACC
LCLAT1	253558	broad.mit.edu;ucsc.edu	GRCh37	2	30863465	30863465	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	157	19			ENST00000309052.4:c.1225A>G	p.Asn409Asp	p.N409D	ENST00000309052	NM_182551.3	409	Aat/Gat	0	0.343	GCCACATTTAAATTCAAAGAA
PDE1A	5136	broad.mit.edu;ucsc.edu	GRCh37	2	183095781	183095781	+	stop_gained	Nonsense_Mutation	SNP	A	A	C			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	255	39			ENST00000435564.1:c.543T>G	p.Tyr181Ter	p.Y181*	ENST00000435564	NM_001258312.1	181	taT/taG	0	0.323	TAAACAGTTCATAAATCATAA
MIB2	142678	broad.mit.edu;ucsc.edu	GRCh37	1	1563188	1563188	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	12	8			ENST00000505820.2:c.2004C>T	p.Arg668=	p.R668=	ENST00000505820		668	cgC/cgT	0	0.692	TGTGTGAGCGCGGCTGTGACG
CELSR1	9620	broad.mit.edu;ucsc.edu	GRCh37	22	46929761	46929761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145654024		TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	359	35			ENST00000262738.3:c.3307G>A	p.Asp1103Asn	p.D1103N	ENST00000262738	NM_014246.1	1103	Gac/Aac	0	0.607	ATCTGGAAGTCGGGCAGCACA
TP53	7157	broad.mit.edu;hgsc.bcm.edu	GRCh37	17	7577101	7577101	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	19	90			ENST00000269305.4:c.837delG	p.Arg280GlufsTer65	p.R280Efs*65	ENST00000269305	NM_001126112.2	279	ggG/gg	0	0.547	GCCGGTCTCTCCCAGGACAGG
ATRX	546	broad.mit.edu;hgsc.bcm.edu	GRCh37	X	76907649	76907650	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-			TCGA-E1-5302-01	TCGA-E1-5302-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	59	180			ENST00000373344.5:c.4511_4512delGA	p.Arg1504GlnfsTer5	p.R1504Qfs*5	ENST00000373344	NM_000489.3	1504	cGA/c	0	0.386	CAATACGTTTTCGTCTCTCTTC
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578		TCGA-CS-6666-01	TCGA-CS-6666-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62	28			ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	0	0.652	GTGGGGGCAGCGCCTCACAAC
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	7578467	7578467	+	missense_variant	Missense_Mutation	SNP	T	T	G			TCGA-CS-6666-01	TCGA-CS-6666-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	48	45			ENST00000269305.4:c.463A>C	p.Thr155Pro	p.T155P	ENST00000269305	NM_001126112.2	155	Acc/Ccc	0	0.612	CGGACGCGGGTGCCGGGCGGG
KRT33A	3883	hgsc.bcm.edu;broad.mit.edu	GRCh37	17	39502881	39502881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148488457		TCGA-CS-6666-01	TCGA-CS-6666-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	89	6			ENST00000007735.3:c.916C>T	p.Arg306Cys	p.R306C	ENST00000007735	NM_004138.3	306	Cgc/Tgc	0	0.587	GAGCTGTAGCGGGCCTCGCTC
DCC	1630	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	18	51025871	51025871	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-CS-6666-01	TCGA-CS-6666-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	124	85			ENST00000442544.2:c.4102T>C	p.Ser1368Pro	p.S1368P	ENST00000442544	NM_005215.3	1368	Tct/Cct	0	0.443	ACCACTTTTGTCTCAGCCAGG
PTPN14	5784	hgsc.bcm.edu;broad.mit.edu	GRCh37	1	214625279	214625279	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-CS-6666-01	TCGA-CS-6666-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	134	9			ENST00000366956.5:c.213G>C	p.Gln71His	p.Q71H	ENST00000366956	NM_005401.4	71	caG/caC	0	0.458	ATCGTGCTTGCTGGCTCTTGC
KIF16B	55614	hgsc.bcm.edu;broad.mit.edu	GRCh37	20	16360692	16360692	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6666-01	TCGA-CS-6666-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	199	12			ENST00000408042.1:c.1955G>A	p.Arg652His	p.R652H	ENST00000408042	NM_001199866.1	652	cGc/cAc	0	0.522	CTCCTGCTTGCGAATCTGGAG
PPP1R16B	26051	hgsc.bcm.edu;broad.mit.edu	GRCh37	20	37547124	37547124	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-CS-6666-01	TCGA-CS-6666-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	72	5			ENST00000299824.1:c.1519G>A	p.Ala507Thr	p.A507T	ENST00000299824	NM_015568.2	507	Gcc/Acc	0	0.612	CAGCAGCATGGCCAGGACGGG
DSCAM	1826	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	21	41496241	41496241	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6666-01	TCGA-CS-6666-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	105	66			ENST00000400454.1:c.3577G>A	p.Ala1193Thr	p.A1193T	ENST00000400454	NM_001271534.1	1193	Gcg/Acg	0	0.597	TTCACACCCGCGGGAGGACCT
TMPRSS2	7113	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	21	42845269	42845269	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-CS-6666-01	TCGA-CS-6666-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9	7			ENST00000398585.3:c.993C>T	p.Ala331=	p.A331=	ENST00000398585	NM_001135099.1	331	gcC/gcT	0	0.692	CGCAGTGGGCGGCTGTCACGA
REL	5966	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	61149057	61149057	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6666-01	TCGA-CS-6666-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84	10			ENST00000295025.8:c.1247C>T	p.Ala416Val	p.A416V	ENST00000295025	NM_002908.2	416	gCc/gTc	0	0.502	TCATCAGTGGCCCACCCCACC
DYNC1I2	1781	hgsc.bcm.edu;broad.mit.edu	GRCh37	2	172586272	172586272	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-CS-6666-01	TCGA-CS-6666-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	141	10			ENST00000397119.3:c.1445T>C	p.Ile482Thr	p.I482T	ENST00000397119	NM_001378.2	482	aTc/aCc	0	0.398	ATCACTGGCATCCATTGTCAT
NBEAL1	65065	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	204003429	204003429	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-CS-6666-01	TCGA-CS-6666-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	246	24			ENST00000449802.1:c.4719G>C	p.Gln1573His	p.Q1573H	ENST00000449802	NM_001114132.1	1573	caG/caC	0	0.373	CTCAAATTCAGATCCAGTTGC
NDUFS1	4719	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	206991481	206991481	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-CS-6666-01	TCGA-CS-6666-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	181	18			ENST00000455934.2:c.2014G>C	p.Asp672His	p.D672H	ENST00000455934	NM_001199984.1	672	Gat/Cat	0	0.393	CCTTCAATATCATCATATCGA
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499		TCGA-CS-6666-01	TCGA-CS-6666-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76	53			ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	0	0.398	TAAGCATGACGACCTATGATG
VIL1	7429	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	219299321	219299321	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-CS-6666-01	TCGA-CS-6666-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	81	68			ENST00000248444.5:c.1573G>A	p.Ala525Thr	p.A525T	ENST00000248444	NM_007127.2	525	Gcc/Acc	0	0.572	GGGAACTGGCGCCAACAACAC
MAB21L2	10586	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	151505024	151505024	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-CS-6666-01	TCGA-CS-6666-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	73	8			ENST00000317605.4:c.843G>C	p.Glu281Asp	p.E281D	ENST00000317605	NM_006439.4	281	gaG/gaC	0	0.627	TGCTGTACGAGTGCGAGAAAC
CTSO	1519	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	156847189	156847189	+	stop_lost	Nonstop_Mutation	SNP	C	C	G			TCGA-CS-6666-01	TCGA-CS-6666-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29	9			ENST00000433477.3:c.965G>C	p.Ter322SerextTer12	p.*322Sext*12	ENST00000433477	NM_001334.2	322	tGa/tCa	0	0.308	CCCAACATGTCACACAAATAT
DNAH5	1767	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	13769245	13769245	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G			TCGA-CS-6666-01	TCGA-CS-6666-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	235	68			ENST00000265104.4:c.9721G>C	p.Val3241Leu	p.V3241L	ENST00000265104	NM_001369.2	3241	Gtc/Ctc	0	0.413	TCTTTTAAGACCTAATTCAAT
KIAA0825	285600	hgsc.bcm.edu;broad.mit.edu	GRCh37	5	93856210	93856210	+	missense_variant	Missense_Mutation	SNP	T	T	G			TCGA-CS-6666-01	TCGA-CS-6666-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	80	6			ENST00000329378.7:c.713A>C	p.Asp238Ala	p.D238A	ENST00000329378	NM_173665.2	238	gAt/gCt	0	0.308	AGCTATTACATCTAAATTTGA
LRRC16A	55604	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	25606448	25606448	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-CS-6666-01	TCGA-CS-6666-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	23	8			ENST00000329474.6:c.3794G>C	p.Ser1265Thr	p.S1265T	ENST00000329474	NM_001173977.1	1265	aGt/aCt	0	0.592	CCCAAACCCAGTCTGGCAGCA
CLIC1	1192	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	31698750	31698750	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-CS-6666-01	TCGA-CS-6666-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	38	20			ENST00000375780.2:c.595A>G	p.Ile199Val	p.I199V	ENST00000375780	NM_001287593.1	199	Atc/Gtc	0	0.582	GCCTCGGGGATGGTGAATCCC
BTNL2	56244	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	32370727	32370727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs79379254		TCGA-CS-6666-01	TCGA-CS-6666-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	24	24			ENST00000454136.3:c.694G>A	p.Val232Ile	p.V232I	ENST00000454136		232	Gtc/Atc	0	0.582	AGGCTGATGACCGACCCCTTC
ABCB1	5243	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	7	87183089	87183089	+	synonymous_variant	Silent	SNP	T	T	C			TCGA-CS-6666-01	TCGA-CS-6666-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	67	49			ENST00000265724.3:c.987A>G	p.Gly329=	p.G329=	ENST00000265724	NM_000927.4	329	ggA/ggG	0	0.378	TGAGTACTTGTCCAATAGAAT
TAS2R4	50832	hgsc.bcm.edu;broad.mit.edu	GRCh37	7	141478489	141478489	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-CS-6666-01	TCGA-CS-6666-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	258	20			ENST00000247881.2:c.201C>G	p.Ile67Met	p.I67M	ENST00000247881	NM_016944.1	67	atC/atG	0	0.443	TGAACACCATCTACTTCGTCT
PLAA	9373	hgsc.bcm.edu;broad.mit.edu	GRCh37	9	26905915	26905915	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-CS-6666-01	TCGA-CS-6666-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64	6			ENST00000397292.3:c.1982G>A	p.Arg661Lys	p.R661K	ENST00000397292	NM_001031689.2	661	aGg/aAg	0	0.458	GCAAAAAGTCCTGAGAGCAAG
AGPAT3	56894	broad.mit.edu;ucsc.edu	GRCh37	21	45379705	45379705	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-CS-6666-01	TCGA-CS-6666-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	34	5			ENST00000398063.2:c.143G>A	p.Arg48His	p.R48H	ENST00000398063	NM_001037553.1	48	cGc/cAc	0	0.667	CTCTACCGCCGCCTCAACTGC
PURG	29942	broad.mit.edu;ucsc.edu	GRCh37	8	30889490	30889490	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-CS-6666-01	TCGA-CS-6666-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	59	58			ENST00000475541.1:c.809A>G	p.Asp270Gly	p.D270G	ENST00000475541	NM_013357.2	270	gAc/gGc	0	0.438	CCTTTTATTGTCCACTCTGAA
ATRX	546	broad.mit.edu;hgsc.bcm.edu	GRCh37	X	76919037	76919038	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T			TCGA-CS-6666-01	TCGA-CS-6666-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3	21			ENST00000373344.5:c.3953dupA	p.Asn1318LysfsTer6	p.N1318Kfs*6	ENST00000373344	NM_000489.3	1318	aat/aaAt	0	0.351	AATTGACTTGATTTTTTGCTTC
DDX24	57062	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	14	94528925	94528925	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-6397-01	TCGA-DU-6397-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	77	23			ENST00000330836.5:c.761C>T	p.Ala254Val	p.A254V	ENST00000330836	NM_020414.3	254	gCg/gTg	0	0.458	CTGCAACACCGCATGAATCAT
NF1	4763	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	29663350	29663350	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C			TCGA-DU-6397-01	TCGA-DU-6397-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	72	6			ENST00000358273.4:c.6007-1G>C		p.X2003_splice	ENST00000358273	NM_001042492.2			0	0.328	TCTTCAACTAGATTACAGATC
CACNA1G	8913	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	48703623	48703623	+	synonymous_variant	Silent	SNP	A	A	G			TCGA-DU-6397-01	TCGA-DU-6397-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	32	13			ENST00000359106.5:c.6645A>G	p.Leu2215=	p.L2215=	ENST00000359106	NM_018896.4	2215	ttA/ttG	0	0.642	GAAGCAGCTTAGAGTTGGACA
SSTR2	6752	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	71166516	71166516	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-DU-6397-01	TCGA-DU-6397-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	54	11			ENST00000357585.2:c.1058C>G	p.Thr353Ser	p.T353S	ENST00000357585	NM_001050.2	353	aCc/aGc	0	0.547	CTGAATGAGACCACGGAGACC
VAV1	7409	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	19	6833209	6833209	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-6397-01	TCGA-DU-6397-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28	16			ENST00000602142.1:c.1523C>T	p.Pro508Leu	p.P508L	ENST00000602142	NM_005428.3	508	cCg/cTg	0	0.438	AACATCTATCCGGAGAATGCC
OR7A5	26659	hgsc.bcm.edu;ucsc.edu	GRCh37	19	14938560	14938560	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-6397-01	TCGA-DU-6397-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30	13			ENST00000322301.3:c.494G>A	p.Arg165Gln	p.R165Q	ENST00000322301		165	cGg/cAg	0	0.443	GAAGGACAGCCGTACTACCAT
FLG	2312	hgsc.bcm.edu;broad.mit.edu	GRCh37	1	152282972	152282972	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-DU-6397-01	TCGA-DU-6397-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	211	17			ENST00000368799.1:c.4390G>C	p.Gly1464Arg	p.G1464R	ENST00000368799	NM_002016.1	1464	Gga/Cga	0	0.572	CCTTGTCTTCCTCCAGTGCTG
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-DU-6397-01	TCGA-DU-6397-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	59	38			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
OR5AC2	81050	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	97806608	97806608	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DU-6397-01	TCGA-DU-6397-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	31	24			ENST00000358642.2:c.592G>A	p.Ala198Thr	p.A198T	ENST00000358642	NM_054106.1	198	Gca/Aca	0	0.289	ATCTATTAACGCACTAATGAT
RETNLB	84666	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	108475916	108475916	+	synonymous_variant	Silent	SNP	G	G	T			TCGA-DU-6397-01	TCGA-DU-6397-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	19	4			ENST00000295755.6:c.117C>A	p.Leu39=	p.L39=	ENST00000295755	NM_032579.2	39	ctC/ctA	0	0.498	CTAGACTGTTGAGAACATCCT
MRPL3	11222	hgsc.bcm.edu;broad.mit.edu	GRCh37	3	131190117	131190117	+	synonymous_variant	Silent	SNP	A	A	C			TCGA-DU-6397-01	TCGA-DU-6397-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	83	4			ENST00000264995.3:c.636T>G	p.Gly212=	p.G212=	ENST00000264995	NM_007208.3	212	ggT/ggG	0	0.403	GAAAACCTTTACCAATACTGA
ALPK1	80216	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	113352721	113352721	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-DU-6397-01	TCGA-DU-6397-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	46	18			ENST00000458497.1:c.2018C>A	p.Pro673His	p.P673H	ENST00000458497	NM_001102406.1	673	cCc/cAc	0	0.493	CCCTTGACACCCTTCTCGCCT
FSTL5	56884	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	162577517	162577517	+	missense_variant	Missense_Mutation	SNP	T	T	C			TCGA-DU-6397-01	TCGA-DU-6397-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	25	14			ENST00000306100.5:c.857A>G	p.Asn286Ser	p.N286S	ENST00000306100	NM_001128427.2	286	aAt/aGt	0	0.353	TAGAATAATATTGTTCCTTTT
FSTL5	56884	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	4	162577525	162577525	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs61746784		TCGA-DU-6397-01	TCGA-DU-6397-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	29	15			ENST00000306100.5:c.849A>T	p.Lys283Asn	p.K283N	ENST00000306100	NM_001128427.2	283	aaA/aaT	0	0.353	TATTGTTCCTTTTCCAGATAA
MCC	4163	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	112439958	112439958	+	synonymous_variant	Silent	SNP	G	G	T	rs142794653	byFrequency	TCGA-DU-6397-01	TCGA-DU-6397-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	117	31			ENST00000408903.3:c.1122C>A	p.Ser374=	p.S374=	ENST00000408903	NM_001085377.1	374	tcC/tcA	0	0.572	CCTCGGCCACGGAGAGGCTGC
UBLCP1	134510	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	158697549	158697549	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-DU-6397-01	TCGA-DU-6397-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	85	9			ENST00000296786.6:c.346C>A	p.Leu116Met	p.L116M	ENST00000296786	NM_145049.3	116	Ctg/Atg	0	0.333	AGAAAACCTACTGAAAATTTC
RREB1	6239	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	7229828	7229828	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DU-6397-01	TCGA-DU-6397-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	264	47			ENST00000379938.2:c.1496C>T	p.Ala499Val	p.A499V	ENST00000379938	NM_001003700.1	499	gCg/gTg	0	0.642	CCACTGCAGGCGATCTTCAAG
GPR115	221393	hgsc.bcm.edu;broad.mit.edu	GRCh37	6	47682356	47682356	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-DU-6397-01	TCGA-DU-6397-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	337	22			ENST00000283303.2:c.1375A>G	p.Ile459Val	p.I459V	ENST00000283303	NM_153838.3	459	Ata/Gta	0	0.458	GTGGTTTATCATAGGCTCTCA
KIT	3815	broad.mit.edu;ucsc.edu	GRCh37	4	55573431	55573431	+	missense_variant	Missense_Mutation	SNP	T	T	A			TCGA-DU-6397-01	TCGA-DU-6397-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	49	20			ENST00000288135.5:c.1093T>A	p.Ser365Thr	p.S365T	ENST00000288135	NM_000222.2	365	Tct/Act	0	0.403	TTATCCCAAGTCTGAGAATGA
OR4M1	441670	broad.mit.edu;ucsc.edu	GRCh37	14	20248557	20248557	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-DU-6397-01	TCGA-DU-6397-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	288	30			ENST00000315957.4:c.76G>T	p.Val26Phe	p.V26F	ENST00000315957	NM_001005500.1	26	Gtc/Ttc	0	0.388	GGTCCAACTAGTCCTATTTGT
RUFY2	55680	broad.mit.edu;ucsc.edu	GRCh37	10	70141155	70141155	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C			TCGA-DU-6397-01	TCGA-DU-6397-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	122	77			ENST00000388768.2:c.1046A>G	p.Asp349Gly	p.D349G	ENST00000388768	NM_017987.4	349	gAt/gGt	0	0.358	ATTCTCTACATCCTGCAATTT
FRMD4B	23150	broad.mit.edu;hgsc.bcm.edu	GRCh37	3	69230517	69230518	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-			TCGA-DU-6397-01	TCGA-DU-6397-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	49	11			ENST00000398540.3:c.2383_2384delAA	p.Lys795GlufsTer21	p.K795Efs*21	ENST00000398540	NM_015123.1	795	AAg/g	0	0.446	CTCCTGACTCTTTGAGTAAACA
C8orf47	203111	broad.mit.edu;hgsc.bcm.edu	GRCh37	8	99101783	99101784	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A			TCGA-DU-6397-01	TCGA-DU-6397-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	28	10			ENST00000318528.3:c.541dupA	p.Thr181AsnfsTer12	p.T181Nfs*12	ENST00000318528	NM_173549.2	180	caa/cAaa	0	0.52	TGAGAATCCACAAACTGCTGCA
SS18	6760	broad.mit.edu;hgsc.bcm.edu	GRCh37	18	23632625	23632626	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-			TCGA-DU-6397-01	TCGA-DU-6397-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	125	32			ENST00000415083.2:c.569_570delAT	p.Tyr190TrpfsTer49	p.Y190Wfs*49	ENST00000415083	NM_001007559.1	190	tAT/t	0	0.426	GTCTGGGACCATAGTTTCCCAT
FUBP1	8880	broad.mit.edu	GRCh37	1	78444677	78444678	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-			TCGA-DU-6397-01	TCGA-DU-6397-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7	10			ENST00000370768.2:c.11_12delAT	p.Tyr4PhefsTer24	p.Y4Ffs*24	ENST00000370768	NM_003902.3	4	tAT/t	0	0.559	GCACTGTTGAATAGTCTGCCAT
CIC	23152	ucsc.edu	GRCh37	19	42791721	42791721	+	missense_variant	Missense_Mutation	SNP	C	C	G			TCGA-DU-6397-01	TCGA-DU-6397-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39	3			ENST00000575354.2:c.607C>G	p.Pro203Ala	p.P203A	ENST00000575354	NM_015125.3	203	Ccc/Gcc	0	0.627	CATCCGGCGGCCCATGAATGC
CIC	23152	ucsc.edu	GRCh37	19	42791790	42791790	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-DU-6397-01	TCGA-DU-6397-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39	3			ENST00000575354.2:c.676G>T	p.Asp226Tyr	p.D226Y	ENST00000575354	NM_015125.3	226	Gac/Tac	0	0.612	TCCCAACCAGGACAACCGGAC
ANKRD30A	91074	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	10	37419199	37419199	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7620-01	TCGA-HT-7620-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	43	10			ENST00000361713.1:c.235G>A	p.Val79Ile	p.V79I	ENST00000361713	NM_052997.2	79	Gta/Ata	0	0.423	TATAAATCTCGTAGATGTGTA
FOXM1	2305	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	2968215	2968215	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-7620-01	TCGA-HT-7620-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	105	22			ENST00000342628.2:c.1995G>A	p.Thr665=	p.T665=	ENST00000342628	NM_202002.2	665	acG/acA	0	0.592	TGGCTGGGGGCGTGAGCCTCC
USP30	84749	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	109519737	109519737	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A			TCGA-HT-7620-01	TCGA-HT-7620-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	128	31			ENST00000257548.5:c.781-1G>A		p.X261_splice	ENST00000257548	NM_032663.3			0	0.428	TCATGCTGTAGGGTCACCCAT
CYP1A2	1544	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	75042314	75042314	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7620-01	TCGA-HT-7620-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39	15			ENST00000343932.4:c.235C>T	p.Arg79Cys	p.R79C	ENST00000343932	NM_000761.3	79	Cgc/Tgc	0	0.672	CCTGCAGATCCGCATTGGCTC
USP31	57478	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	23080559	23080559	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7620-01	TCGA-HT-7620-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	150	16			ENST00000219689.7:c.2867G>A	p.Arg956His	p.R956H	ENST00000219689	NM_020718.3	956	cGc/cAc	0	0.552	GTTCAATCTGCGGGTGTCCGA
PRSS54	221191	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	16	58324928	58324928	+	missense_variant	Missense_Mutation	SNP	G	G	T			TCGA-HT-7620-01	TCGA-HT-7620-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76	18			ENST00000219301.4:c.198C>A	p.His66Gln	p.H66Q	ENST00000219301	NM_001080492.1	66	caC/caA	0	0.607	CGAAAGCCAGGTGTGTGTACT
FUBP1	8880	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	78429792	78429792	+	stop_gained	Nonsense_Mutation	SNP	A	A	T			TCGA-HT-7620-01	TCGA-HT-7620-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99	29			ENST00000370768.2:c.996T>A	p.Cys332Ter	p.C332*	ENST00000370768	NM_003902.3	332	tgT/tgA	0	0.328	CAGCATGTTGACATCGGTCTG
CFH	3075	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	196648911	196648911	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7620-01	TCGA-HT-7620-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	34	6			ENST00000367429.4:c.778C>T	p.Pro260Ser	p.P260S	ENST00000367429	NM_000186.3	260	Cct/Tct	0	0.294	GCGTCCGTTGCCTTCATGTGA
CNST	163882	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	246810446	246810446	+	missense_variant	Missense_Mutation	SNP	A	A	G			TCGA-HT-7620-01	TCGA-HT-7620-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	42	14			ENST00000366513.4:c.943A>G	p.Lys315Glu	p.K315E	ENST00000366513	NM_152609.2	315	Aaa/Gaa	0	0.388	TTTAGAGAGTAAAACTTGTCT
CCT7	10574	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	73478419	73478419	+	stop_gained	Nonsense_Mutation	SNP	C	C	G			TCGA-HT-7620-01	TCGA-HT-7620-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95	30			ENST00000258091.5:c.1269C>G	p.Tyr423Ter	p.Y423*	ENST00000258091	NM_006429.3	423	taC/taG	0	0.517	TGCGGGATTACTCAAGGACTA
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-HT-7620-01	TCGA-HT-7620-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	70	16			ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	0	0.393	ATAAGCATGACGACCTATGAT
SRD5A1	6715	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	6663021	6663021	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7620-01	TCGA-HT-7620-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	84	25			ENST00000274192.5:c.655G>A	p.Ala219Thr	p.A219T	ENST00000274192	NM_001047.2	219	Gcg/Acg	0	0.408	TGTCCAAGGCGCGGCTTTTGC
GRIA1	2890	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	153175109	153175109	+	intron_variant	Intron	SNP	T	T	C			TCGA-HT-7620-01	TCGA-HT-7620-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	51	10			ENST00000518783.1:c.2415+814T>C		*805*	ENST00000518783	NM_001258021.1			0	0.473	CAAATGGTGGTACGATAAAGG
SLC34A1	6569	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	176825109	176825109	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-HT-7620-01	TCGA-HT-7620-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	70	21			ENST00000324417.5:c.1742G>A	p.Arg581His	p.R581H	ENST00000324417	NM_003052.4	581	cGc/cAc	0	0.667	TTCCTGCCTCGCTGGATGCAC
SCAND3	114821	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	28540669	28540669	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7620-01	TCGA-HT-7620-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	87	19			ENST00000452236.2:c.2997C>T	p.Cys999=	p.C999=	ENST00000452236	NM_052923.1	999	tgC/tgT	0	0.328	gatgaatgaagcaatgtgttg
TFAP2B	7021	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	50807962	50807962	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-HT-7620-01	TCGA-HT-7620-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	87	12			ENST00000393655.3:c.1034C>A	p.Thr345Lys	p.T345K	ENST00000393655	NM_003221.3	345	aCa/aAa	0	0.517	CGGCAGCACACAGACCCGAGT
LAMA2	3908	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	6	129823889	129823889	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-HT-7620-01	TCGA-HT-7620-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	49	9			ENST00000421865.2:c.8330C>T	p.Ala2777Val	p.A2777V	ENST00000421865	NM_001079823.1	2777	gCa/gTa	0	0.408	ATTGCAATTGCATTTGATGAC
CLIC2	1193	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	X	154508571	154508571	+	stop_gained	Nonsense_Mutation	SNP	A	A	C			TCGA-HT-7620-01	TCGA-HT-7620-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	16	20			ENST00000369449.2:c.449T>G	p.Leu150Ter	p.L150*	ENST00000369449	NM_001289.4	150	tTa/tGa	0	0.408	TGGGGTGTTTAAGTAGTCATC
CAMK2D	817	broad.mit.edu;ucsc.edu	GRCh37	4	114436309	114436309	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-HT-7620-01	TCGA-HT-7620-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	70	16			ENST00000342666.5:c.735C>T	p.Ala245=	p.A245=	ENST00000342666		245	gcC/gcT	0	0.398	TGAGGTCTTTGGCTTCAGGAG
DHX35	60625	broad.mit.edu;ucsc.edu	GRCh37	20	37634881	37634881	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-HT-7620-01	TCGA-HT-7620-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	263	65			ENST00000252011.3:c.1104C>T	p.Tyr368=	p.Y368=	ENST00000252011	NM_021931.3	368	taC/taT	0	0.522	TCCGAGCCTACAATCCCAGGA
PIK3CA	5290	broad.mit.edu	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-			TCGA-HT-7620-01	TCGA-HT-7620-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	38	9			ENST00000263967.3:c.328_330delGAA	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	0	0.34	AGGCAACCGTGAAGAAAAGATCC
NLRP14	338323	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	11	7064302	7064302	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DH-5141-01	TCGA-DH-5141-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	209	27			ENST00000299481.4:c.1045G>A	p.Ala349Thr	p.A349T	ENST00000299481	NM_176822.3	349	Gcc/Acc	0	0.428	TAAGAGGTGGGCCATGAAAGT
NCKAP1L	3071	hgsc.bcm.edu;ucsc.edu	GRCh37	12	54914539	54914539	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DH-5141-01	TCGA-DH-5141-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	495	231			ENST00000293373.6:c.1687C>T	p.Arg563Cys	p.R563C	ENST00000293373	NM_005337.4	563	Cgt/Tgt	0	0.463	TGCCATGTTGCGTTATGCCAT
LGR5	8549	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	12	71978453	71978453	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DH-5141-01	TCGA-DH-5141-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	187	95			ENST00000266674.5:c.2663C>T	p.Pro888Leu	p.P888L	ENST00000266674	NM_001277226.1	888	cCa/cTa	0	0.458	GTGCCATCACCAGCTTATCCA
IDH2	3418	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503		TCGA-DH-5141-01	TCGA-DH-5141-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	82	51			ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	0	0.632	ATGGGCGTGCCTGCCAATGGT
KRT36	8689	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	17	39642800	39642800	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DH-5141-01	TCGA-DH-5141-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	27	5			ENST00000328119.6:c.1232C>T	p.Thr411Met	p.T411M	ENST00000328119	NM_003771.4	411	aCg/aTg	0	0.577	CTTGCATGCCGTGGCACAAGG
CDH20	28316	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	18	59174700	59174700	+	synonymous_variant	Silent	SNP	G	G	A			TCGA-DH-5141-01	TCGA-DH-5141-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	144	15			ENST00000262717.4:c.924G>A	p.Glu308=	p.E308=	ENST00000262717		308	gaG/gaA	0	0.433	TCAATGCAGAGATGAAATATA
SERPINB3	6317	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	18	61323264	61323264	+	missense_variant	Missense_Mutation	SNP	A	A	C			TCGA-DH-5141-01	TCGA-DH-5141-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	131	29			ENST00000283752.5:c.800T>G	p.Met267Arg	p.M267R	ENST00000283752	NM_006919.2	267	aTg/aGg	0	0.378	TGTCCATTCCATCAATTTCTC
GBP5	115362	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	89728016	89728016	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DH-5141-01	TCGA-DH-5141-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	80	66			ENST00000343435.5:c.1534G>A	p.Glu512Lys	p.E512K	ENST00000343435	NM_001134486.2	512	Gag/Aag	0	0.463	ATCATTTGCTCGTTCTGCCTT
PCNXL2	80003	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	1	233344354	233344354	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DH-5141-01	TCGA-DH-5141-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	93	14			ENST00000258229.9:c.2773G>A	p.Ala925Thr	p.A925T	ENST00000258229	NM_014801.3	925	Gcc/Acc	0	0.423	CTGGCTTTGGCCCCTGTATCA
PCSK2	5126	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	20	17434533	17434533	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-DH-5141-01	TCGA-DH-5141-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	152	26			ENST00000262545.2:c.1032C>T	p.Asp344=	p.D344=	ENST00000262545	NM_002594.3	344	gaC/gaT	0	0.597	CCCTGTACGACGAGAGCTGCT
PI4KA	5297	hgsc.bcm.edu;broad.mit.edu	GRCh37	22	21115635	21115635	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DH-5141-01	TCGA-DH-5141-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	127	11			ENST00000255882.6:c.2748G>A	p.Met916Ile	p.M916I	ENST00000255882	NM_058004.3	916	atG/atA	0	0.368	AGTAGCAGAACATTACCTGGA
SPECC1L	23384	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	22	24717648	24717648	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DH-5141-01	TCGA-DH-5141-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	187	86			ENST00000314328.9:c.700C>T	p.His234Tyr	p.H234Y	ENST00000314328	NM_015330.4	234	Cac/Tac	0	0.438	TATTATGGCTCACCAGCCGAC
C2orf71	388939	hgsc.bcm.edu;broad.mit.edu	GRCh37	2	29294007	29294007	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DH-5141-01	TCGA-DH-5141-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	91	41			ENST00000331664.5:c.3121C>T	p.Pro1041Ser	p.P1041S	ENST00000331664	NM_001029883.2	1041	Cca/Tca	0	0.687	GTGGTGGGTGGGCTTAGCACC
RIF1	55183	hgsc.bcm.edu;broad.mit.edu	GRCh37	2	152293371	152293371	+	missense_variant	Missense_Mutation	SNP	C	C	A			TCGA-DH-5141-01	TCGA-DH-5141-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	120	11			ENST00000243326.5:c.1226C>A	p.Thr409Asn	p.T409N	ENST00000243326		409	aCt/aAt	0	0.418	GCCCCGGGAACTCCCCGAATG
CHRNA1	1134	hgsc.bcm.edu;broad.mit.edu	GRCh37	2	175614763	175614763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852804		TCGA-DH-5141-01	TCGA-DH-5141-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	148	9			ENST00000261007.5:c.988G>A	p.Val330Ile	p.V330I	ENST00000261007	NM_001039523.2	330	Gtc/Atc	0	0.537	GAGGCAATGACGAACACCATG
PLXNB1	5364	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	3	48461210	48461210	+	missense_variant	Missense_Mutation	SNP	G	G	C			TCGA-DH-5141-01	TCGA-DH-5141-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	14	7			ENST00000358536.4:c.2485C>G	p.Pro829Ala	p.P829A	ENST00000358536	NM_002673.4	829	Cca/Gca	0	0.701	ATGGCCCCTGGGAAAGTGGTG
NIPBL	25836	hgsc.bcm.edu;broad.mit.edu	GRCh37	5	37008732	37008732	+	stop_gained	Nonsense_Mutation	SNP	C	C	G			TCGA-DH-5141-01	TCGA-DH-5141-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	224	12			ENST00000282516.8:c.4328C>G	p.Ser1443Ter	p.S1443*	ENST00000282516	NM_133433.3	1443	tCa/tGa	0	0.274	CAGGTATTCTCAAGATATGAA
C5orf34	375444	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	5	43506030	43506030	+	stop_gained	Nonsense_Mutation	SNP	C	C	T			TCGA-DH-5141-01	TCGA-DH-5141-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	269	22			ENST00000306862.2:c.752G>A	p.Trp251Ter	p.W251*	ENST00000306862	NM_198566.2	251	tGg/tAg	0	0.408	AGGATATTTCCATTCCTCTGG
ADRB2	154	hgsc.bcm.edu;broad.mit.edu	GRCh37	5	148206922	148206922	+	synonymous_variant	Silent	SNP	C	C	T			TCGA-DH-5141-01	TCGA-DH-5141-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	288	20			ENST00000305988.4:c.528C>T	p.Ala176=	p.A176=	ENST00000305988	NM_000024.5	176	gcC/gcT	0	0.537	GGTACCGGGCCACCCACCAGG
GRM1	2911	hgsc.bcm.edu;broad.mit.edu	GRCh37	6	146720659	146720659	+	synonymous_variant	Silent	SNP	G	G	C			TCGA-DH-5141-01	TCGA-DH-5141-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	128	9			ENST00000361719.2:c.2484G>C	p.Gly828=	p.G828=	ENST00000361719		828	ggG/ggC	0	0.488	TGGCTCTGGGGTGCATGTTCA
RALYL	138046	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	8	85774590	85774590	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DH-5141-01	TCGA-DH-5141-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	49	7			ENST00000517638.1:c.512G>A	p.Arg171His	p.R171H	ENST00000517638	NM_001100391.1	171	cGt/cAt	0	0.507	CCGCTGAAGCGTCCCAGAGTG
KLF4	9314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	GRCh37	9	110249405	110249405	+	missense_variant	Missense_Mutation	SNP	G	G	A			TCGA-DH-5141-01	TCGA-DH-5141-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	177	88			ENST00000374672.4:c.1168C>T	p.Arg390Trp	p.R390W	ENST00000374672	NM_004235.4	390	Cgg/Tgg	0	0.587	GTCCTTTTCCGGGGCCACGAT
CHMP1A	5119	broad.mit.edu;ucsc.edu	GRCh37	16	89715806	89715806	+	missense_variant	Missense_Mutation	SNP	C	C	T			TCGA-DH-5141-01	TCGA-DH-5141-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	151	70			ENST00000397901.3:c.205G>A	p.Val69Ile	p.V69I	ENST00000397901	NM_002768.4	69	Gta/Ata	0	0.597	ACTGCGTCTACGCGGGACGCC