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| author | elixir-it |
|---|---|
| date | Mon, 01 Oct 2018 11:21:05 -0400 |
| parents | 786c9295d2be |
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#version 2.4 Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand 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 Tumor_Sample_UUID Matched_Norm_Sample_UUID HGVSc HGVSp HGVSp_Short Transcript_ID Exon_Number t_depth t_ref_count t_alt_count n_depth n_ref_count n_alt_count all_effects Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation ALLELE_NUM DISTANCE STRAND_VEP SYMBOL SYMBOL_SOURCE HGNC_ID BIOTYPE CANONICAL CCDS ENSP SWISSPROT TREMBL UNIPARC RefSeq SIFT PolyPhen EXON INTRON DOMAINS AF AFR_AF AMR_AF ASN_AF EAS_AF EUR_AF SAS_AF AA_AF EA_AF CLIN_SIG SOMATIC PUBMED MOTIF_NAME MOTIF_POS HIGH_INF_POS MOTIF_SCORE_CHANGE IMPACT PICK VARIANT_CLASS TSL HGVS_OFFSET PHENO MINIMISED ExAC_AF ExAC_AF_AFR ExAC_AF_AMR ExAC_AF_EAS ExAC_AF_FIN ExAC_AF_NFE ExAC_AF_OTH ExAC_AF_SAS GENE_PHENO FILTER flanking_bps variant_id variant_qual ExAC_AF_Adj ExAC_AC_AN_Adj ExAC_AC_AN ExAC_AC_AN_AFR ExAC_AC_AN_AMR ExAC_AC_AN_EAS ExAC_AC_AN_FIN ExAC_AC_AN_NFE ExAC_AC_AN_OTH ExAC_AC_AN_SAS ExAC_FILTER gnomAD_AF gnomAD_AFR_AF gnomAD_AMR_AF gnomAD_ASJ_AF gnomAD_EAS_AF gnomAD_FIN_AF gnomAD_NFE_AF gnomAD_OTH_AF gnomAD_SAS_AF CICP27 0 . GRCh38 chr1 133129 133129 + RNA SNP G G A rs367730352 TUMOR NORMAL G G n.2105G>A ENST00000442987 1/1 907 610 296 376 311 65 RP11-34P13.7,intron_variant,,ENST00000610542,;RP11-34P13.7,intron_variant,,ENST00000453576,;RP11-34P13.7,upstream_gene_variant,,ENST00000471248,;RP11-34P13.7,upstream_gene_variant,,ENST00000477740,;CICP27,non_coding_transcript_exon_variant,,ENST00000442987,;RP11-34P13.15,downstream_gene_variant,,ENST00000494149,;RP11-34P13.16,downstream_gene_variant,,ENST00000595919,; A ENSG00000233750 ENST00000442987 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 2105/3812 rs367730352 1 1 CICP27 HGNC HGNC:48835 processed_pseudogene YES 1/1 MODIFIER 1 SNV . TGT . . CICP27 0 . GRCh38 chr1 133160 133160 + RNA SNP G G A rs371468694 TUMOR NORMAL G G n.2136G>A ENST00000442987 1/1 871 724 145 351 305 46 RP11-34P13.7,intron_variant,,ENST00000610542,;RP11-34P13.7,intron_variant,,ENST00000453576,;RP11-34P13.7,upstream_gene_variant,,ENST00000471248,;RP11-34P13.7,upstream_gene_variant,,ENST00000477740,;CICP27,non_coding_transcript_exon_variant,,ENST00000442987,;RP11-34P13.15,downstream_gene_variant,,ENST00000494149,;RP11-34P13.16,downstream_gene_variant,,ENST00000595919,; A ENSG00000233750 ENST00000442987 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 2136/3812 rs371468694 1 1 CICP27 HGNC HGNC:48835 processed_pseudogene YES 1/1 MODIFIER 1 SNV . GGG . . CICP27 0 . GRCh38 chr1 133483 133483 + RNA SNP G G T rs369820305 TUMOR NORMAL G G n.2459G>T ENST00000442987 1/1 1101 822 278 388 314 72 RP11-34P13.7,non_coding_transcript_exon_variant,,ENST00000610542,;RP11-34P13.7,non_coding_transcript_exon_variant,,ENST00000453576,;RP11-34P13.7,upstream_gene_variant,,ENST00000471248,;RP11-34P13.7,upstream_gene_variant,,ENST00000477740,;CICP27,non_coding_transcript_exon_variant,,ENST00000442987,;RP11-34P13.15,downstream_gene_variant,,ENST00000494149,;RP11-34P13.16,downstream_gene_variant,,ENST00000595919,; T ENSG00000233750 ENST00000442987 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 2459/3812 rs369820305 1 1 CICP27 HGNC HGNC:48835 processed_pseudogene YES 1/1 MODIFIER 1 SNV . CGG . . FAM132A 0 . GRCh38 chr1 1250144 1250144 + 5'Flank SNP T T C rs115270700 TUMOR NORMAL T T ENST00000330388 18 15 3 10 10 0 UBE2J2,downstream_gene_variant,,ENST00000347370,NM_194458.1;UBE2J2,downstream_gene_variant,,ENST00000349431,NM_058167.2;UBE2J2,downstream_gene_variant,,ENST00000400929,NM_194457.1;FAM132A,upstream_gene_variant,,ENST00000330388,NM_001014980.2;RP5-902P8.12,non_coding_transcript_exon_variant,,ENST00000565563,;UBE2J2,downstream_gene_variant,,ENST00000450390,;UBE2J2,downstream_gene_variant,,ENST00000464036,;,regulatory_region_variant,,ENSR00000000162,; C ENSG00000184163 ENST00000330388 Transcript upstream_gene_variant -/1036 -/909 -/302 rs115270700 1 3422 -1 FAM132A HGNC HGNC:32308 protein_coding YES CCDS30554.1 ENSP00000329137 Q5T7M4 UPI00001D7E7A NM_001014980.2 C:0.0877 C:0.0613 C:0.0504 C:0.1647 C:0.0666 C:0.0920 MODIFIER 1 SNV 1 . ATA . . SKI 0 . GRCh38 chr1 2280653 2280653 + Intron SNP A A G rs186058331 TUMOR NORMAL A A c.970-22325A>G ENST00000378536 70 34 36 55 40 15 SKI,intron_variant,,ENST00000378536,NM_003036.3;SKI,intron_variant,,ENST00000478223,;SKI,intron_variant,,ENST00000508416,; G ENSG00000157933 ENST00000378536 Transcript intron_variant -/5613 -/2187 -/728 rs186058331 1 1 SKI HGNC HGNC:10896 protein_coding YES CCDS39.1 ENSP00000367797 P12755 UPI00001359DE NM_003036.3 1/6 MODIFIER 1 SNV 1 1 . CAC . . SKI 0 . GRCh38 chr1 2280736 2280736 + Intron SNP A A G novel TUMOR NORMAL A A c.970-22242A>G ENST00000378536 8 5 3 8 8 0 SKI,intron_variant,,ENST00000378536,NM_003036.3;SKI,intron_variant,,ENST00000478223,;SKI,intron_variant,,ENST00000508416,; G ENSG00000157933 ENST00000378536 Transcript intron_variant -/5613 -/2187 -/728 1 1 SKI HGNC HGNC:10896 protein_coding YES CCDS39.1 ENSP00000367797 P12755 UPI00001359DE NM_003036.3 1/6 MODIFIER 1 SNV 1 1 . GAG . . DISP3 0 . GRCh38 chr1 11522650 11522650 + Intron SNP G A A rs371097095 TUMOR NORMAL G G c.2363-1292G>A ENST00000294484 2 1 1 6 6 0 DISP3,intron_variant,,ENST00000294484,NM_020780.1;,regulatory_region_variant,,ENSR00000001409,; A ENSG00000204624 ENST00000294484 Transcript intron_variant -/5215 -/4179 -/1392 rs371097095 1 1 DISP3 HGNC HGNC:29251 protein_coding YES CCDS41247.1 ENSP00000294484 Q9P2K9 UPI00001C1D7A NM_020780.1 10/20 MODIFIER 1 SNV 1 . GGG . . DAB1 0 . GRCh38 chr1 57636120 57636120 + Intron SNP C C A rs12079557 TUMOR NORMAL C C n.625+13472G>T ENST00000485760 44 28 16 34 26 8 DAB1,intron_variant,,ENST00000485760,; A ENSG00000173406 ENST00000485760 Transcript intron_variant,non_coding_transcript_variant -/2668 rs12079557 1 -1 DAB1 HGNC HGNC:2661 processed_transcript 7/20 MODIFIER 1 SNV 2 . ACA . . NEGR1 0 . GRCh38 chr1 72135390 72135390 + Intron SNP C C A rs796166092 TUMOR NORMAL C C c.176+146929G>T ENST00000357731 90 64 26 53 43 10 NEGR1,intron_variant,,ENST00000357731,NM_173808.2; A ENSG00000172260 ENST00000357731 Transcript intron_variant -/12811 -/1065 -/354 rs796166092 1 -1 NEGR1 HGNC HGNC:17302 protein_coding YES CCDS661.1 ENSP00000350364 Q7Z3B1 UPI00000477EE NM_173808.2 1/6 MODIFIER 1 SNV 1 . ACA . . IGSF3 0 . GRCh38 chr1 116600445 116600445 + Intron SNP G G A rs59940339 TUMOR NORMAL G G c.1685-100C>T ENST00000369483 30 20 10 24 22 2 IGSF3,intron_variant,,ENST00000369483,NM_001542.3;IGSF3,intron_variant,,ENST00000369486,NM_001007237.2;IGSF3,intron_variant,,ENST00000318837,; A ENSG00000143061 ENST00000369483 Transcript intron_variant -/7326 -/3645 -/1214 rs59940339 1 -1 IGSF3 HGNC HGNC:5950 protein_coding YES CCDS30814.1 ENSP00000358495 O75054 UPI0000140437 NM_001542.3 7/11 A:0.0960 A:0.1271 A:0.1023 A:0.1200 A:0.0467 A:0.0757 MODIFIER 1 SNV 5 1 . GGA . . IGSF3 0 . GRCh38 chr1 116600446 116600446 + Intron SNP A A G rs57198501 TUMOR NORMAL A A c.1685-101T>C ENST00000369483 29 20 9 22 22 0 IGSF3,intron_variant,,ENST00000369483,NM_001542.3;IGSF3,intron_variant,,ENST00000369486,NM_001007237.2;IGSF3,intron_variant,,ENST00000318837,; G ENSG00000143061 ENST00000369483 Transcript intron_variant -/7326 -/3645 -/1214 rs57198501 1 -1 IGSF3 HGNC HGNC:5950 protein_coding YES CCDS30814.1 ENSP00000358495 O75054 UPI0000140437 NM_001542.3 7/11 G:0.0960 G:0.1271 G:0.1023 G:0.1200 G:0.0467 G:0.0757 MODIFIER 1 SNV 5 1 . GAC . . ENSR00000012648 0 . GRCh38 chr1 125167865 125167865 + IGR SNP T C C novel TUMOR NORMAL T T ENSR00000012648 1 0 1 4 4 0 ,regulatory_region_variant,,ENSR00000012648,; C ENSR00000012648 RegulatoryFeature regulatory_region_variant 1 TF_binding_site MODIFIER 1 SNV . TTC . . ENSR00000012650 0 . GRCh38 chr1 143192820 143192820 + IGR SNP G A A novel TUMOR NORMAL G G ENSR00000012650 2 1 1 6 6 0 ,regulatory_region_variant,,ENSR00000012650,; A ENSR00000012650 RegulatoryFeature regulatory_region_variant 1 TF_binding_site MODIFIER 1 SNV . CGA . . ENSR00000012650 0 . GRCh38 chr1 143192836 143192836 + IGR SNP C T T novel TUMOR NORMAL C C ENSR00000012650 2 1 1 6 6 0 ,regulatory_region_variant,,ENSR00000012650,; T ENSR00000012650 RegulatoryFeature regulatory_region_variant 1 TF_binding_site MODIFIER 1 SNV . ACG . . LINC00624 0 . GRCh38 chr1 147517696 147517696 + RNA SNP C C T rs12046574 TUMOR NORMAL C C n.180G>A ENST00000621316 1/4 9 5 4 6 6 0 LINC00624,non_coding_transcript_exon_variant,,ENST00000621316,;LINC00624,non_coding_transcript_exon_variant,,ENST00000619867,; T ENSG00000278811 ENST00000621316 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 180/3372 rs12046574 1 -1 LINC00624 HGNC HGNC:44254 antisense YES 1/4 T:0.3027 T:0.2042 T:0.4726 T:0.2321 T:0.3569 T:0.3323 MODIFIER 1 SNV 1 . CCT . . LINC01138 0 . GRCh38 chr1 148359371 148359371 + 3'Flank SNP C C A novel TUMOR NORMAL C C ENST00000622328 15 12 3 8 8 0 LINC01138,downstream_gene_variant,,ENST00000622328,;RP6-74O6.6,upstream_gene_variant,,ENST00000609678,;RNVU1-1,downstream_gene_variant,,ENST00000384610,; A ENSG00000274020 ENST00000622328 Transcript downstream_gene_variant -/2212 1 3624 -1 LINC01138 HGNC HGNC:49454 lincRNA YES MODIFIER 1 SNV 2 . TCA . . NBPF19 0 . GRCh38 chr1 149390829 149390829 + 5'UTR SNP C C A novel TUMOR NORMAL C C c.-1064C>A ENST00000621744 1/97 39 23 16 33 12 20 NBPF19,5_prime_UTR_variant,,ENST00000621744,;,regulatory_region_variant,,ENSR00000013370,; A ENSG00000271383 ENST00000621744 Transcript 5_prime_UTR_variant 207/14425 -/11532 -/3843 1 1 NBPF19 HGNC HGNC:31999 protein_coding YES ENSP00000478752 A0A087WUL8 UPI000387BE73 1/97 MODIFIER 1 SNV 5 . GCG . . TMOD4 0 . GRCh38 chr1 151171163 151171163 + Intron SNP A G G novel TUMOR NORMAL A A c.727-100T>C ENST00000295314 1 0 1 2 2 0 TMOD4,intron_variant,,ENST00000295314,NM_013353.2;TMOD4,intron_variant,,ENST00000466891,;SCNM1,downstream_gene_variant,,ENST00000368905,NM_024041.3;SCNM1,downstream_gene_variant,,ENST00000368902,NM_001204856.1;SCNM1,downstream_gene_variant,,ENST00000602841,NM_001204848.1;TMOD4,downstream_gene_variant,,ENST00000441701,;SCNM1,downstream_gene_variant,,ENST00000461862,;SCNM1,downstream_gene_variant,,ENST00000497147,;TMOD4,downstream_gene_variant,,ENST00000601585,;SCNM1,downstream_gene_variant,,ENST00000459799,;SCNM1,downstream_gene_variant,,ENST00000471039,;TMOD4,downstream_gene_variant,,ENST00000488488,;VPS72,intron_variant,,ENST00000491094,;TMOD4,intron_variant,,ENST00000463543,; G ENSG00000163157 ENST00000295314 Transcript intron_variant -/1267 -/1038 -/345 1 -1 TMOD4 HGNC HGNC:11874 protein_coding YES CCDS988.1 ENSP00000295314 Q9NZQ9 UPI00000015C0 NM_013353.2 7/9 MODIFIER 1 SNV 1 . GAG . . FLG 0 . GRCh38 chr1 152303901 152303901 + Missense_Mutation SNP C C G rs75235053 TUMOR NORMAL C C c.10985G>C p.Ser3662Thr p.S3662T ENST00000368799 3/3 2572 1975 595 563 445 117 FLG,missense_variant,p.Ser3662Thr,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; G ENSG00000143631 ENST00000368799 Transcript missense_variant 11021/12747 10985/12186 3662/4061 S/T aGt/aCt rs75235053 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 deleterious(0.01) unknown(0) 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571,Pfam_domain:PF03516 MODERATE 1 SNV 1 1 . ACT . . FLG 0 . GRCh38 chr1 152303983 152303983 + Missense_Mutation SNP C C T rs75448155 TUMOR NORMAL C C c.10903G>A p.Asp3635Asn p.D3635N ENST00000368799 3/3 2851 2065 786 614 516 98 FLG,missense_variant,p.Asp3635Asn,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; T ENSG00000143631 ENST00000368799 Transcript missense_variant 10939/12747 10903/12186 3635/4061 D/N Gac/Aac rs75448155 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 deleterious(0) unknown(0) 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571,Pfam_domain:PF03516 T:0.0268 T:0.103 MODERATE 1 SNV 1 1 . TCT . . FLG 0 . GRCh38 chr1 152304107 152304107 + Missense_Mutation SNP C C G rs12083389 TUMOR NORMAL C C c.10779G>C p.Glu3593Asp p.E3593D ENST00000368799 3/3 1708 1357 351 394 368 26 FLG,missense_variant,p.Glu3593Asp,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; G ENSG00000143631 ENST00000368799 Transcript missense_variant 10815/12747 10779/12186 3593/4061 E/D gaG/gaC rs12083389 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 tolerated(1) unknown(0) 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571 G:0.3614 G:0.4796 G:0.3213 G:0.4732 G:0.1233 G:0.3599 G:0.3795 G:0.0319 MODERATE 1 SNV 1 1 . TCT . . FLG 0 . GRCh38 chr1 152304122 152304122 + Silent SNP G G A rs12742178 TUMOR NORMAL G G c.10764C>T p.= p.H3588= ENST00000368799 3/3 1605 1281 324 389 370 19 FLG,synonymous_variant,p.=,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; A ENSG00000143631 ENST00000368799 Transcript synonymous_variant 10800/12747 10764/12186 3588/4061 H caC/caT rs12742178 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571 A:0.0887 A:0.0227 A:0.0965 A:0.1984 A:0.0199 A:0.1299 LOW 1 SNV 1 1 . CGT . . FLG 0 . GRCh38 chr1 152304150 152304150 + Missense_Mutation SNP G G C rs3126075 TUMOR NORMAL G G c.10736C>G p.Thr3579Arg p.T3579R ENST00000368799 3/3 1470 1215 255 433 348 85 FLG,missense_variant,p.Thr3579Arg,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; C ENSG00000143631 ENST00000368799 Transcript missense_variant 10772/12747 10736/12186 3579/4061 T/R aCg/aGg rs3126075 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 tolerated(0.57) unknown(0) 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571 C:0.4778 C:0.6074 C:0.4395 C:0.6498 C:0.1561 C:0.4836 C:0.2548 C:0.0174 MODERATE 1 SNV 1 1 . CGT . . FLG 0 . GRCh38 chr1 152306079 152306079 + Missense_Mutation SNP T T C rs80221306 TUMOR NORMAL T T c.8807A>G p.Asp2936Gly p.D2936G ENST00000368799 3/3 3958 3206 750 578 408 170 FLG,missense_variant,p.Asp2936Gly,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; C ENSG00000143631 ENST00000368799 Transcript missense_variant 8843/12747 8807/12186 2936/4061 D/G gAc/gGc rs80221306 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 tolerated(0.38) benign(0.003) 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571 C:0.0734 C:0.0964 MODERATE 1 SNV 1 1 . GTC . . FLG 0 . GRCh38 chr1 152306338 152306338 + Missense_Mutation SNP C C T rs2184952 TUMOR NORMAL C C c.8548G>A p.Gly2850Ser p.G2850S ENST00000368799 3/3 4985 4176 804 411 302 109 FLG,missense_variant,p.Gly2850Ser,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; T ENSG00000143631 ENST00000368799 Transcript missense_variant 8584/12747 8548/12186 2850/4061 G/S Ggc/Agc rs2184952 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 tolerated(0.85) possibly_damaging(0.579) 3/3 Low_complexity_(Seg):seg,Pfam_domain:PF03516 T:0.0768 T:0.0521 MODERATE 1 SNV 1 1 . CCG . . FLG 0 . GRCh38 chr1 152306380 152306380 + Missense_Mutation SNP T T G rs11582087 TUMOR NORMAL T T c.8506A>C p.Ser2836Arg p.S2836R ENST00000368799 3/3 5056 4057 998 487 431 56 FLG,missense_variant,p.Ser2836Arg,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; G ENSG00000143631 ENST00000368799 Transcript missense_variant 8542/12747 8506/12186 2836/4061 S/R Agt/Cgt rs11582087 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 deleterious(0.04) possibly_damaging(0.766) 3/3 Low_complexity_(Seg):seg G:0.0314 G:0.1107 MODERATE 1 SNV 1 1 . CTT . . FLG 0 . GRCh38 chr1 152307694 152307694 + Missense_Mutation SNP C C G rs71625201 TUMOR NORMAL C C c.7192G>C p.Glu2398Gln p.E2398Q ENST00000368799 3/3 2374 1465 909 537 412 125 FLG,missense_variant,p.Glu2398Gln,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; G ENSG00000143631 ENST00000368799 Transcript missense_variant 7228/12747 7192/12186 2398/4061 E/Q Gag/Cag rs71625201 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 tolerated(0.37) benign(0.403) 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571 G:0.3305 G:0.1135 G:0.4092 G:0.5665 G:0.1690 G:0.4908 G:0.1326 G:0.1657 MODERATE 1 SNV 1 1 . TCT . . FLG 0 . GRCh38 chr1 152307789 152307789 + Missense_Mutation SNP C C G rs71625202 TUMOR NORMAL C C c.7097G>C p.Ser2366Thr p.S2366T ENST00000368799 3/3 2091 1480 609 574 431 142 FLG,missense_variant,p.Ser2366Thr,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; G ENSG00000143631 ENST00000368799 Transcript missense_variant 7133/12747 7097/12186 2366/4061 S/T aGt/aCt rs71625202 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 deleterious(0.01) benign(0.418) 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571,Pfam_domain:PF03516 G:0.0348 G:0.1329 MODERATE 1 SNV 1 1 . ACT . . FLG 0 . GRCh38 chr1 152307871 152307871 + Missense_Mutation SNP C C T rs139476473 TUMOR NORMAL C C c.7015G>A p.Asp2339Asn p.D2339N ENST00000368799 3/3 1915 1498 415 445 416 27 FLG,missense_variant,p.Asp2339Asn,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; T ENSG00000143631 ENST00000368799 Transcript missense_variant 7051/12747 7015/12186 2339/4061 D/N Gac/Aac rs139476473 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 deleterious(0.02) possibly_damaging(0.822) 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571,Pfam_domain:PF03516 T:0.0185 T:0.0328 MODERATE 1 SNV 1 1 . TCT . . FLG 0 . GRCh38 chr1 152307896 152307896 + Silent SNP G G A rs6664985 TUMOR NORMAL G G c.6990C>T p.= p.H2330= ENST00000368799 3/3 1801 1180 620 367 367 0 FLG,synonymous_variant,p.=,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; A ENSG00000143631 ENST00000368799 Transcript synonymous_variant 7026/12747 6990/12186 2330/4061 H caC/caT rs6664985 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571,Pfam_domain:PF03516 A:0.4535 A:0.4902 A:0.4524 A:0.6567 A:0.1730 A:0.4836 LOW 1 SNV 1 1 . CGT . . FLG 0 . GRCh38 chr1 152307995 152307995 + Missense_Mutation SNP C C G rs78179835 TUMOR NORMAL C C c.6891G>C p.Glu2297Asp p.E2297D ENST00000368799 3/3 3096 2226 869 429 340 89 FLG,missense_variant,p.Glu2297Asp,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; G ENSG00000143631 ENST00000368799 Transcript missense_variant 6927/12747 6891/12186 2297/4061 E/D gaG/gaC rs78179835 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 tolerated(1) benign(0.217) 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571 G:0.0915 G:0.1071 MODERATE 1 SNV 1 1 . TCT . . FLG 0 . GRCh38 chr1 152308083 152308083 + Missense_Mutation SNP T T C rs150122015 TUMOR NORMAL T T c.6803A>G p.His2268Arg p.H2268R ENST00000368799 3/3 2559 2246 311 422 374 46 FLG,missense_variant,p.His2268Arg,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; C ENSG00000143631 ENST00000368799 Transcript missense_variant 6839/12747 6803/12186 2268/4061 H/R cAt/cGt rs150122015 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 tolerated(0.28) benign(0.227) 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571 MODERATE 1 SNV 1 1 . ATG . . FLG 0 . GRCh38 chr1 152308424 152308424 + Missense_Mutation SNP T T G rs74129452 TUMOR NORMAL T T c.6462A>C p.Gln2154His p.Q2154H ENST00000368799 3/3 3124 2189 933 422 345 77 FLG,missense_variant,p.Gln2154His,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; G ENSG00000143631 ENST00000368799 Transcript missense_variant 6498/12747 6462/12186 2154/4061 Q/H caA/caC rs74129452 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 tolerated(1) benign(0.216) 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571 G:0.3438 G:0.3843 G:0.3487 G:0.4444 G:0.1541 G:0.3773 MODERATE 1 SNV 1 1 . CTT . . FLG 0 . GRCh38 chr1 152308814 152308814 + Silent SNP A A G rs80353812 TUMOR NORMAL A A c.6072T>C p.= p.H2024= ENST00000368799 3/3 3521 2338 1182 424 296 127 FLG,synonymous_variant,p.=,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;FLG-AS1,upstream_gene_variant,,ENST00000392688,; G ENSG00000143631 ENST00000368799 Transcript synonymous_variant 6108/12747 6072/12186 2024/4061 H caT/caC rs80353812 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571,Pfam_domain:PF03516 G:0.3281 G:0.3850 G:0.3343 G:0.4355 G:0.1292 G:0.3405 G:0.2624 G:0.1262 LOW 1 SNV 1 1 . CAT . . FLG 0 . GRCh38 chr1 152310807 152310807 + Missense_Mutation SNP C C T rs11586631 TUMOR NORMAL C C c.4079G>A p.Arg1360His p.R1360H ENST00000368799 3/3 2461 1314 1140 394 322 70 FLG,missense_variant,p.Arg1360His,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;FLG-AS1,upstream_gene_variant,,ENST00000392688,; T ENSG00000143631 ENST00000368799 Transcript missense_variant 4115/12747 4079/12186 1360/4061 R/H cGc/cAc rs11586631 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 tolerated(0.83) possibly_damaging(0.812) 3/3 Pfam_domain:PF03516 T:0.2877 T:0.0144 T:0.3890 T:0.5823 T:0.1421 T:0.4315 T:0.037 T:0.1439 MODERATE 1 SNV 1 1 . GCG . . SPTA1 0 . GRCh38 chr1 158607804 158607804 + 3'Flank SNP C C A novel TUMOR NORMAL C C ENST00000368147 10 8 2 8 8 0 SPTA1,downstream_gene_variant,,ENST00000368147,NM_003126.2;OR10Z1,downstream_gene_variant,,ENST00000361284,NM_001004478.1;SPTA1,downstream_gene_variant,,ENST00000485680,;SPTA1,downstream_gene_variant,,ENST00000481212,;SPTA1,downstream_gene_variant,,ENST00000498708,; A ENSG00000163554 ENST00000368147 Transcript downstream_gene_variant -/7999 -/7260 -/2419 1 2902 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 MODIFIER 1 SNV 1 1 . ACT . . SDHC 0 . GRCh38 chr1 161363118 161363118 + 3'UTR SNP C C T rs138085670 TUMOR NORMAL C C c.*685C>T ENST00000367975 6/6 326 189 137 171 125 46 SDHC,3_prime_UTR_variant,,ENST00000367975,NM_003001.3;SDHC,3_prime_UTR_variant,,ENST00000342751,NM_001035511.1;CFAP126,downstream_gene_variant,,ENST00000367974,NM_001013625.3;SDHC,downstream_gene_variant,,ENST00000432287,NM_001035512.1;SDHC,downstream_gene_variant,,ENST00000392169,NM_001035513.1;SDHC,downstream_gene_variant,,ENST00000513009,NM_001278172.1;SDHC,upstream_gene_variant,,ENST00000437833,;SDHC,downstream_gene_variant,,ENST00000470743,;SDHC,downstream_gene_variant,,ENST00000504963,; T ENSG00000143252 ENST00000367975 Transcript 3_prime_UTR_variant 1344/13566 -/510 -/169 rs138085670 1 1 SDHC HGNC HGNC:10682 protein_coding YES CCDS1230.1 ENSP00000356953 Q99643 A0A0S2Z4B7 UPI0000001636 NM_003001.3 6/6 T:0.0204 T:0.0023 T:0.0014 T:0.0446 T:0.0000 T:0.0542 MODIFIER 1 SNV 1 1 . TCT . . RP11-122G18.10 0 . GRCh38 chr1 161444478 161444478 + Intron SNP T T A rs3123349 TUMOR NORMAL T T n.55-16459A>T ENST00000637155 85 54 31 90 60 30 RP11-122G18.10,intron_variant,,ENST00000637155,;RP11-122G18.11,upstream_gene_variant,,ENST00000636824,; A ENSG00000283360 ENST00000637155 Transcript intron_variant,non_coding_transcript_variant -/863 rs3123349 1 -1 RP11-122G18.10 Clone_based_vega_gene lincRNA YES 1/4 MODIFIER 1 SNV . CTG . . RP11-122G18.10 0 . GRCh38 chr1 161444486 161444486 + Intron SNP A A G rs540204255 TUMOR NORMAL A A n.55-16467T>C ENST00000637155 73 42 31 86 56 30 RP11-122G18.10,intron_variant,,ENST00000637155,;RP11-122G18.11,upstream_gene_variant,,ENST00000636824,; G ENSG00000283360 ENST00000637155 Transcript intron_variant,non_coding_transcript_variant -/863 rs540204255 1 -1 RP11-122G18.10 Clone_based_vega_gene lincRNA YES 1/4 G:0.0004 G:0.0000 G:0.0000 G:0.0000 G:0.0010 G:0.0010 MODIFIER 1 SNV . CAC . . RP11-122G18.10 0 . GRCh38 chr1 161444488 161444488 + Intron SNP A A G rs12076971 TUMOR NORMAL A A n.55-16469T>C ENST00000637155 74 43 31 88 57 31 RP11-122G18.10,intron_variant,,ENST00000637155,;RP11-122G18.11,upstream_gene_variant,,ENST00000636824,; G ENSG00000283360 ENST00000637155 Transcript intron_variant,non_coding_transcript_variant -/863 rs12076971 1 -1 RP11-122G18.10 Clone_based_vega_gene lincRNA YES 1/4 G:0.0004 G:0.0000 G:0.0000 G:0.0000 G:0.0010 G:0.0010 MODIFIER 1 SNV . CAC . . RP11-122G18.10 0 . GRCh38 chr1 161444514 161444514 + Intron SNP T T A rs765889351 TUMOR NORMAL T T n.55-16495A>T ENST00000637155 70 35 35 99 70 29 RP11-122G18.10,intron_variant,,ENST00000637155,;RP11-122G18.11,upstream_gene_variant,,ENST00000636824,; A ENSG00000283360 ENST00000637155 Transcript intron_variant,non_coding_transcript_variant -/863 rs765889351 1 -1 RP11-122G18.10 Clone_based_vega_gene lincRNA YES 1/4 MODIFIER 1 SNV . CTC . . RP11-122G18.10 0 . GRCh38 chr1 161444527 161444527 + Intron SNP C C G novel TUMOR NORMAL C C n.55-16508G>C ENST00000637155 74 53 21 125 103 22 RP11-122G18.10,intron_variant,,ENST00000637155,;RP11-122G18.11,upstream_gene_variant,,ENST00000636824,; G ENSG00000283360 ENST00000637155 Transcript intron_variant,non_coding_transcript_variant -/863 1 -1 RP11-122G18.10 Clone_based_vega_gene lincRNA YES 1/4 MODIFIER 1 SNV . TCT . . RALGPS2 0 . GRCh38 chr1 178725267 178725267 + 5'UTR SNP G G A novel TUMOR NORMAL G G c.-236G>A ENST00000367635 1/20 10 7 3 10 10 0 RALGPS2,5_prime_UTR_variant,,ENST00000367634,NM_001286247.1;RALGPS2,5_prime_UTR_variant,,ENST00000367635,NM_152663.4;RALGPS2,upstream_gene_variant,,ENST00000324778,;RP11-428K3.1,non_coding_transcript_exon_variant,,ENST00000608517,;RALGPS2,non_coding_transcript_exon_variant,,ENST00000495034,;,regulatory_region_variant,,ENSR00000016375,; A ENSG00000116191 ENST00000367635 Transcript 5_prime_UTR_variant 103/5834 -/1752 -/583 1 1 RALGPS2 HGNC HGNC:30279 protein_coding YES CCDS1325.1 ENSP00000356607 Q86X27 UPI000000DBE1 NM_152663.4 1/20 MODIFIER 1 SNV 1 . CGG . . ADORA1 0 . GRCh38 chr1 203166324 203166324 + 3'UTR SNP C C T rs16851030 TUMOR NORMAL C C c.*424C>T ENST00000367236 3/3 8 6 2 6 6 0 ADORA1,3_prime_UTR_variant,,ENST00000367236,NM_001048230.1;ADORA1,3_prime_UTR_variant,,ENST00000337894,NM_000674.2;ADORA1,3_prime_UTR_variant,,ENST00000309502,;ADORA1,3_prime_UTR_variant,,ENST00000367235,;MYBPH,downstream_gene_variant,,ENST00000255416,NM_004997.2;MYBPH,downstream_gene_variant,,ENST00000621380,;ADORA1,downstream_gene_variant,,ENST00000618295,;ADORA1,non_coding_transcript_exon_variant,,ENST00000472535,;ADORA1,downstream_gene_variant,,ENST00000467253,;ADORA1,downstream_gene_variant,,ENST00000464019,;,regulatory_region_variant,,ENSR00000018401,; T ENSG00000163485 ENST00000367236 Transcript 3_prime_UTR_variant 2326/3407 -/981 -/326 rs16851030 1 1 ADORA1 HGNC HGNC:262 protein_coding YES CCDS1434.1 ENSP00000356205 P30542 UPI00000503E1 NM_001048230.1 3/3 T:0.1532 T:0.1142 T:0.1009 T:0.3958 T:0.0368 T:0.1125 20520601,21886579,22462821,19019667,24003382 MODIFIER 1 SNV 1 . CCC . . CICP13 0 . GRCh38 chr1 222468242 222468242 + RNA SNP T C C rs4103697 TUMOR NORMAL T T n.149T>C ENST00000422015 1/1 84 8 76 61 56 5 CICP13,non_coding_transcript_exon_variant,,ENST00000422015,; C ENSG00000234419 ENST00000422015 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 149/2789 rs4103697 1 1 CICP13 HGNC HGNC:37907 processed_pseudogene YES 1/1 T:0.0385 C:0.9418 C:0.9539 C:0.9663 C:0.9742 C:0.9755 MODIFIER 1 SNV . ATG . . GTF2IP20 0 . GRCh38 chr1 223947556 223947556 + 3'Flank SNP G G A rs61825417 TUMOR NORMAL G G ENST00000634905 65 45 20 91 71 20 GTF2IP20,downstream_gene_variant,,ENST00000634905,;GTF2IP20,downstream_gene_variant,,ENST00000608760,;CICP5,upstream_gene_variant,,ENST00000424045,; A ENSG00000272645 ENST00000634905 Transcript downstream_gene_variant -/2966 rs61825417 1 3923 -1 GTF2IP20 HGNC HGNC:51732 processed_transcript YES A:0.2630 A:0.3154 A:0.2637 A:0.0794 A:0.4125 A:0.2270 MODIFIER 1 SNV 5 . CGA . . GTF2IP20 0 . GRCh38 chr1 223947588 223947588 + 3'Flank SNP G T T rs573572074 TUMOR NORMAL G G ENST00000634905 87 63 24 117 103 14 GTF2IP20,downstream_gene_variant,,ENST00000634905,;GTF2IP20,downstream_gene_variant,,ENST00000608760,;CICP5,upstream_gene_variant,,ENST00000424045,; T ENSG00000272645 ENST00000634905 Transcript downstream_gene_variant -/2966 rs573572074 1 3891 -1 GTF2IP20 HGNC HGNC:51732 processed_transcript YES T:0.0974 T:0.0787 T:0.1023 T:0.0208 T:0.1958 T:0.0971 MODIFIER 1 SNV 5 . TGC . . GTF2IP20 0 . GRCh38 chr1 223947978 223947978 + 3'Flank SNP G G T rs61825418 TUMOR NORMAL G G ENST00000634905 430 225 205 254 191 63 GTF2IP20,downstream_gene_variant,,ENST00000634905,;GTF2IP20,downstream_gene_variant,,ENST00000608760,;CICP5,non_coding_transcript_exon_variant,,ENST00000424045,; T ENSG00000272645 ENST00000634905 Transcript downstream_gene_variant -/2966 rs61825418 1 3501 -1 GTF2IP20 HGNC HGNC:51732 processed_transcript YES T:0.2616 T:0.2912 T:0.2651 T:0.1002 T:0.4125 T:0.2301 MODIFIER 1 SNV 5 . AGT . . GTF2IP20 0 . GRCh38 chr1 223948062 223948062 + 3'Flank SNP G G A rs61825419 TUMOR NORMAL G G ENST00000634905 1124 586 537 304 198 104 GTF2IP20,downstream_gene_variant,,ENST00000634905,;GTF2IP20,downstream_gene_variant,,ENST00000608760,;CICP5,non_coding_transcript_exon_variant,,ENST00000424045,; A ENSG00000272645 ENST00000634905 Transcript downstream_gene_variant -/2966 rs61825419 1 3417 -1 GTF2IP20 HGNC HGNC:51732 processed_transcript YES A:0.3319 A:0.4024 A:0.3112 A:0.1627 A:0.4473 A:0.3067 MODIFIER 1 SNV 5 . CGC . . GTF2IP20 0 . GRCh38 chr1 223948558 223948558 + 3'Flank SNP C C T rs78538264 TUMOR NORMAL C C ENST00000634905 154 74 80 40 35 5 GTF2IP20,downstream_gene_variant,,ENST00000634905,;GTF2IP20,downstream_gene_variant,,ENST00000608760,;CICP5,non_coding_transcript_exon_variant,,ENST00000424045,; T ENSG00000272645 ENST00000634905 Transcript downstream_gene_variant -/2966 rs78538264 1 2921 -1 GTF2IP20 HGNC HGNC:51732 processed_transcript YES MODIFIER 1 SNV 5 . ACG . . GTF2IP20 0 . GRCh38 chr1 223949699 223949699 + 3'Flank SNP T T C rs3991993 TUMOR NORMAL T T ENST00000634905 370 206 164 189 189 0 GTF2IP20,downstream_gene_variant,,ENST00000634905,;GTF2IP20,downstream_gene_variant,,ENST00000608760,;CICP5,non_coding_transcript_exon_variant,,ENST00000424045,; C ENSG00000272645 ENST00000634905 Transcript downstream_gene_variant -/2966 rs3991993 1 1780 -1 GTF2IP20 HGNC HGNC:51732 processed_transcript YES MODIFIER 1 SNV 5 . GTG . . GTF2IP20 0 . GRCh38 chr1 223950486 223950486 + 3'Flank SNP C C T rs3991971 TUMOR NORMAL C C ENST00000634905 115 25 90 79 18 61 GTF2IP20,downstream_gene_variant,,ENST00000634905,;GTF2IP20,downstream_gene_variant,,ENST00000608760,;CICP5,downstream_gene_variant,,ENST00000424045,; T ENSG00000272645 ENST00000634905 Transcript downstream_gene_variant -/2966 rs3991971 1 993 -1 GTF2IP20 HGNC HGNC:51732 processed_transcript YES MODIFIER 1 SNV 5 . ACG . . CICP26 0 . GRCh38 chr1 227976709 227976709 + RNA SNP T C C rs61825104 TUMOR NORMAL T T n.1485A>G ENST00000425003 1/3 91 4 86 10 10 0 CICP26,non_coding_transcript_exon_variant,,ENST00000425003,;SEPT14P17,upstream_gene_variant,,ENST00000617978,; C ENSG00000233003 ENST00000425003 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 1485/2448 rs61825104 1 -1 CICP26 HGNC HGNC:48834 unprocessed_pseudogene YES 1/3 MODIFIER 1 SNV . CTA . . CICP26 0 . GRCh38 chr1 227977309 227977309 + RNA SNP A A G rs9662308 TUMOR NORMAL A A n.885T>C ENST00000425003 1/3 461 236 225 170 131 38 CICP26,non_coding_transcript_exon_variant,,ENST00000425003,;SEPT14P17,upstream_gene_variant,,ENST00000617978,; G ENSG00000233003 ENST00000425003 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 885/2448 rs9662308 1 -1 CICP26 HGNC HGNC:48834 unprocessed_pseudogene YES 1/3 G:0.2290 G:0.3714 G:0.1787 G:0.2708 G:0.0517 G:0.2117 MODIFIER 1 SNV . CAT . . RP11-443B7.3 0 . GRCh38 chr1 234978406 234978406 + 3'Flank SNP C G G novel TUMOR NORMAL C C ENST00000549744 1 0 1 2 2 0 RP11-443B7.3,downstream_gene_variant,,ENST00000549744,; G ENSG00000258082 ENST00000549744 Transcript downstream_gene_variant -/846 1 1241 -1 RP11-443B7.3 Clone_based_vega_gene lincRNA YES MODIFIER 1 SNV 3 . CCA . . RP11-443B7.3 0 . GRCh38 chr1 234978426 234978426 + 3'Flank SNP C G G novel TUMOR NORMAL C C ENST00000549744 1 0 1 2 2 0 RP11-443B7.3,downstream_gene_variant,,ENST00000549744,; G ENSG00000258082 ENST00000549744 Transcript downstream_gene_variant -/846 1 1221 -1 RP11-443B7.3 Clone_based_vega_gene lincRNA YES MODIFIER 1 SNV 3 . GCA . . RP11-443B7.3 0 . GRCh38 chr1 234978429 234978429 + 3'Flank SNP T C C novel TUMOR NORMAL T T ENST00000549744 1 0 1 2 2 0 RP11-443B7.3,downstream_gene_variant,,ENST00000549744,; C ENSG00000258082 ENST00000549744 Transcript downstream_gene_variant -/846 1 1218 -1 RP11-443B7.3 Clone_based_vega_gene lincRNA YES MODIFIER 1 SNV 3 . CTC . . FMN2 0 . GRCh38 chr1 240207797 240207797 + Silent SNP G G A rs71646827 TUMOR NORMAL G G c.2985G>A p.= p.A995= ENST00000319653 5/18 245 180 64 161 133 26 FMN2,synonymous_variant,p.=,ENST00000319653,NM_020066.4,NM_001305424.1;FMN2,downstream_gene_variant,,ENST00000447095,; A ENSG00000155816 ENST00000319653 Transcript synonymous_variant 3215/6434 2985/5169 995/1722 A gcG/gcA rs71646827 1 1 FMN2 HGNC HGNC:14074 protein_coding YES CCDS31069.2 ENSP00000318884 Q9NZ56 UPI00015FA087 NM_020066.4,NM_001305424.1 5/18 Pfam_domain:PF06346,Prints_domain:PR01217,Low_complexity_(Seg):seg,SMART_domains:SM00498 LOW 1 SNV 5 1 . CGG . . FMN2 0 . GRCh38 chr1 240207800 240207800 + Silent SNP C C A rs71646887 TUMOR NORMAL C C c.2988C>A p.= p.G996= ENST00000319653 5/18 225 167 53 152 126 22 FMN2,synonymous_variant,p.=,ENST00000319653,NM_020066.4,NM_001305424.1;FMN2,downstream_gene_variant,,ENST00000447095,; A ENSG00000155816 ENST00000319653 Transcript synonymous_variant 3218/6434 2988/5169 996/1722 G ggC/ggA rs71646887 1 1 FMN2 HGNC HGNC:14074 protein_coding YES CCDS31069.2 ENSP00000318884 Q9NZ56 UPI00015FA087 NM_020066.4,NM_001305424.1 5/18 Pfam_domain:PF06346,Prints_domain:PR01217,Low_complexity_(Seg):seg,SMART_domains:SM00498 LOW 1 SNV 5 1 . GCA . . FMN2 0 . GRCh38 chr1 240207806 240207806 + Silent SNP C C T rs11586155 TUMOR NORMAL C C c.2994C>T p.= p.P998= ENST00000319653 5/18 216 164 51 144 122 21 FMN2,synonymous_variant,p.=,ENST00000319653,NM_020066.4,NM_001305424.1;FMN2,downstream_gene_variant,,ENST00000447095,; T ENSG00000155816 ENST00000319653 Transcript synonymous_variant 3224/6434 2994/5169 998/1722 P ccC/ccT rs11586155 1 1 FMN2 HGNC HGNC:14074 protein_coding YES CCDS31069.2 ENSP00000318884 Q9NZ56 UPI00015FA087 NM_020066.4,NM_001305424.1 5/18 Pfam_domain:PF06346,Prints_domain:PR01217,Low_complexity_(Seg):seg,SMART_domains:SM00498 LOW 1 SNV 5 1 . CCC . . FMN2 0 . GRCh38 chr1 240207812 240207812 + Silent SNP G T A rs71646889 TUMOR NORMAL G T c.3000G>A p.= p.P1000= ENST00000319653 5/18 185 16 31 124 37 12 FMN2,synonymous_variant,p.=,ENST00000319653,NM_020066.4,NM_001305424.1;FMN2,downstream_gene_variant,,ENST00000447095,; A ENSG00000155816 ENST00000319653 Transcript synonymous_variant 3230/6434 3000/5169 1000/1722 P ccG/ccA rs71646889 1 1 FMN2 HGNC HGNC:14074 protein_coding YES CCDS31069.2 ENSP00000318884 Q9NZ56 UPI00015FA087 NM_020066.4,NM_001305424.1 5/18 Pfam_domain:PF06346,Prints_domain:PR01217,Low_complexity_(Seg):seg,SMART_domains:SM00498 T:0.2678 T:0.3570 T:0.1873 T:0.2927 T:0.2008 T:0.2474 LOW 1 SNV 5 1 . CGC . . FMN2 0 . GRCh38 chr1 240208175 240208175 + Silent SNP T T G rs200682272 TUMOR NORMAL T T c.3363T>G p.= p.P1121= ENST00000319653 5/18 146 111 30 125 101 17 FMN2,synonymous_variant,p.=,ENST00000319653,NM_020066.4,NM_001305424.1;FMN2,downstream_gene_variant,,ENST00000447095,; G ENSG00000155816 ENST00000319653 Transcript synonymous_variant 3593/6434 3363/5169 1121/1722 P ccT/ccG rs200682272 1 1 FMN2 HGNC HGNC:14074 protein_coding YES CCDS31069.2 ENSP00000318884 Q9NZ56 UPI00015FA087 NM_020066.4,NM_001305424.1 5/18 Pfam_domain:PF06346,hmmpanther:PTHR13037,Low_complexity_(Seg):seg,SMART_domains:SM00498 LOW 1 SNV 5 1 . CTC . . FMN2 0 . GRCh38 chr1 240472659 240472659 + Intron SNP G G T rs1953603 TUMOR NORMAL G G c.5142+206G>T ENST00000319653 7 5 2 6 6 0 FMN2,intron_variant,,ENST00000319653,NM_020066.4,NM_001305424.1;FMN2,intron_variant,,ENST00000543681,;FMN2,intron_variant,,ENST00000545751,;FMN2,intron_variant,,ENST00000496950,; T ENSG00000155816 ENST00000319653 Transcript intron_variant -/6434 -/5169 -/1722 rs1953603 1 1 FMN2 HGNC HGNC:14074 protein_coding YES CCDS31069.2 ENSP00000318884 Q9NZ56 UPI00015FA087 NM_020066.4,NM_001305424.1 17/17 T:0.2965 T:0.0923 T:0.4092 T:0.4702 T:0.3280 T:0.2812 MODIFIER 1 SNV 5 1 . AGA . . Unknown 0 . GRCh38 chr1 242810191 242810191 + IGR SNP T T G rs2780803 TUMOR NORMAL T T 171 99 72 71 56 15 G intergenic_variant rs2780803 1 MODIFIER 1 SNV . TTT . . Unknown 0 . GRCh38 chr1 242810198 242810198 + IGR SNP T T G rs865863353 TUMOR NORMAL T T 177 95 82 79 58 21 G intergenic_variant rs865863353 1 MODIFIER 1 SNV . TTT . . LINC01347 0 . GRCh38 chr1 243052907 243052907 + 3'Flank SNP C C T rs375705608 TUMOR NORMAL C C ENST00000627498 17 11 6 7 7 0 LINC01347,upstream_gene_variant,,ENST00000437691,;LINC01347,downstream_gene_variant,,ENST00000627498,;RP11-261C10.8,downstream_gene_variant,,ENST00000611420,;RP11-261C10.7,downstream_gene_variant,,ENST00000517560,; T ENSG00000214837 ENST00000627498 Transcript downstream_gene_variant -/3841 rs375705608 1 3400 -1 LINC01347 HGNC HGNC:50566 processed_transcript YES MODIFIER 1 SNV 1 . CCG . . Unknown 0 . GRCh38 chr1 244891249 244891249 + IGR SNP C C T rs528047174 TUMOR NORMAL C C 7 5 2 6 6 0 T intergenic_variant rs528047174 1 T:0.3173 T:0.3321 T:0.3084 T:0.3284 T:0.3241 T:0.2853 MODIFIER 1 SNV . TCT . . LINC01250 0 . GRCh38 chr2 3035112 3035112 + Intron SNP T T C rs6749589 TUMOR NORMAL T T n.439-68437N>G ENST00000457478 559 401 157 263 202 59 LINC01250,intron_variant,,ENST00000457478,; C ENSG00000234423 ENST00000457478 Transcript intron_variant,non_coding_transcript_variant -/2344 rs6749589 1 -1 LINC01250 HGNC HGNC:49844 lincRNA YES 3/6 MODIFIER 1 SNV 2 . GTG . . TSSC1 0 . GRCh38 chr2 3329166 3329166 + Intron SNP G G C rs71279311 TUMOR NORMAL G G c.259+8851N>G ENST00000382125 64 47 13 66 54 12 TSSC1,intron_variant,,ENST00000398659,;TSSC1,intron_variant,,ENST00000443925,;TSSC1,intron_variant,,ENST00000382125,NM_003310.2;TSSC1,intron_variant,,ENST00000441271,;TSSC1,intron_variant,,ENST00000444776,;TSSC1,intron_variant,,ENST00000463662,;TSSC1,intron_variant,,ENST00000455162,;TSSC1,intron_variant,,ENST00000406835,;TSSC1,intron_variant,,ENST00000435721,; C ENSG00000032389 ENST00000382125 Transcript intron_variant -/1766 -/1164 -/387 rs71279311 1 -1 TSSC1 HGNC HGNC:12383 protein_coding YES CCDS1651.1 ENSP00000371559 Q53HC9 UPI000006DFE1 NM_003310.2 3/8 MODIFIER 1 SNV 1 . AGG . . TSSC1 0 . GRCh38 chr2 3329223 3329223 + Intron SNP G G C rs74188699 TUMOR NORMAL G G c.259+8794N>G ENST00000382125 36 22 7 34 27 7 TSSC1,intron_variant,,ENST00000398659,;TSSC1,intron_variant,,ENST00000443925,;TSSC1,intron_variant,,ENST00000382125,NM_003310.2;TSSC1,intron_variant,,ENST00000441271,;TSSC1,intron_variant,,ENST00000444776,;TSSC1,intron_variant,,ENST00000463662,;TSSC1,intron_variant,,ENST00000455162,;TSSC1,intron_variant,,ENST00000406835,;TSSC1,intron_variant,,ENST00000435721,; C ENSG00000032389 ENST00000382125 Transcript intron_variant -/1766 -/1164 -/387 rs74188699 1 -1 TSSC1 HGNC HGNC:12383 protein_coding YES CCDS1651.1 ENSP00000371559 Q53HC9 UPI000006DFE1 NM_003310.2 3/8 MODIFIER 1 SNV 1 . AGG . . TSSC1 0 . GRCh38 chr2 3329230 3329230 + Intron SNP G G A rs13004833 TUMOR NORMAL G G c.259+8787N>T ENST00000382125 31 18 12 30 21 7 TSSC1,intron_variant,,ENST00000398659,;TSSC1,intron_variant,,ENST00000443925,;TSSC1,intron_variant,,ENST00000382125,NM_003310.2;TSSC1,intron_variant,,ENST00000441271,;TSSC1,intron_variant,,ENST00000444776,;TSSC1,intron_variant,,ENST00000463662,;TSSC1,intron_variant,,ENST00000455162,;TSSC1,intron_variant,,ENST00000406835,;TSSC1,intron_variant,,ENST00000435721,; A ENSG00000032389 ENST00000382125 Transcript intron_variant -/1766 -/1164 -/387 rs13004833 1 -1 TSSC1 HGNC HGNC:12383 protein_coding YES CCDS1651.1 ENSP00000371559 Q53HC9 UPI000006DFE1 NM_003310.2 3/8 MODIFIER 1 SNV 1 . AGT . . TSSC1 0 . GRCh38 chr2 3329243 3329243 + Intron SNP A A G rs113258696 TUMOR NORMAL A A c.259+8774N>C ENST00000382125 31 20 11 29 27 2 TSSC1,intron_variant,,ENST00000398659,;TSSC1,intron_variant,,ENST00000443925,;TSSC1,intron_variant,,ENST00000382125,NM_003310.2;TSSC1,intron_variant,,ENST00000441271,;TSSC1,intron_variant,,ENST00000444776,;TSSC1,intron_variant,,ENST00000463662,;TSSC1,intron_variant,,ENST00000455162,;TSSC1,intron_variant,,ENST00000406835,;TSSC1,intron_variant,,ENST00000435721,; G ENSG00000032389 ENST00000382125 Transcript intron_variant -/1766 -/1164 -/387 rs113258696 1 -1 TSSC1 HGNC HGNC:12383 protein_coding YES CCDS1651.1 ENSP00000371559 Q53HC9 UPI000006DFE1 NM_003310.2 3/8 G:0.3021 G:0.3351 G:0.1643 G:0.4514 G:0.2167 G:0.2894 MODIFIER 1 SNV 1 . CAC . . DCDC2C 0 . GRCh38 chr2 3775131 3775131 + Intron SNP G G C rs371674744 TUMOR NORMAL G G c.955-3685N>C ENST00000399143 366 254 112 172 129 43 DCDC2C,intron_variant,,ENST00000399143,NM_001287444.1;DCDC2C,intron_variant,,ENST00000423741,;DCDC2C,intron_variant,,ENST00000537457,; C ENSG00000214866 ENST00000399143 Transcript intron_variant -/1480 -/1095 -/364 rs371674744 1 1 DCDC2C HGNC HGNC:32696 protein_coding YES CCDS74481.1 ENSP00000382097 A8MYV0 UPI0002742D44 NM_001287444.1 8/10 MODIFIER 1 SNV 5 . TGT . . CYS1 0 . GRCh38 chr2 10080680 10080680 + 5'Flank SNP C C T novel TUMOR NORMAL C C ENST00000381813 5 3 2 6 6 0 CYS1,upstream_gene_variant,,ENST00000381813,NM_001037160.2;AC104794.4,upstream_gene_variant,,ENST00000425235,;CYS1,intron_variant,,ENST00000477304,; T ENSG00000205795 ENST00000381813 Transcript upstream_gene_variant -/2738 -/477 -/158 1 269 -1 CYS1 HGNC HGNC:18525 protein_coding YES CCDS33145.1 ENSP00000371234 Q717R9 UPI00001D6281 NM_001037160.2 MODIFIER 1 SNV 1 . CCC . . WDR35 0 . GRCh38 chr2 19985338 19985338 + Intron SNP C C T novel TUMOR NORMAL C C c.143-2804N>A ENST00000345530 32 20 11 41 23 16 WDR35,intron_variant,,ENST00000345530,NM_001006657.1;WDR35,intron_variant,,ENST00000281405,NM_020779.3;AC079145.4,upstream_gene_variant,,ENST00000416575,;WDR35,intron_variant,,ENST00000414212,; T ENSG00000118965 ENST00000345530 Transcript intron_variant -/6960 -/3546 -/1181 1 -1 WDR35 HGNC HGNC:29250 protein_coding YES CCDS33152.1 ENSP00000314444 Q9P2L0 UPI000034E5D3 NM_001006657.1 2/27 MODIFIER 1 SNV 1 1 . CCA . . MAP4K3 0 . GRCh38 chr2 39404606 39404606 + Intron SNP C C T rs374072817 TUMOR NORMAL C C c.97-26483N>A ENST00000263881 10 6 4 6 6 0 MAP4K3,intron_variant,,ENST00000263881,NM_003618.3;MAP4K3,intron_variant,,ENST00000341681,NM_001270425.1;MAP4K3,intron_variant,,ENST00000484274,;MAP4K3,intron_variant,,ENST00000429397,;MAP4K3,intron_variant,,ENST00000437968,; T ENSG00000011566 ENST00000263881 Transcript intron_variant -/4362 -/2685 -/894 rs374072817 1 -1 MAP4K3 HGNC HGNC:6865 protein_coding YES CCDS1803.1 ENSP00000263881 Q8IVH8 UPI00000747E6 NM_003618.3 1/33 MODIFIER 1 SNV 1 . TCT . . MAP4K3 0 . GRCh38 chr2 39404609 39404609 + Intron SNP C C T rs113384156 TUMOR NORMAL C C c.97-26486N>A ENST00000263881 9 5 4 6 6 0 MAP4K3,intron_variant,,ENST00000263881,NM_003618.3;MAP4K3,intron_variant,,ENST00000341681,NM_001270425.1;MAP4K3,intron_variant,,ENST00000484274,;MAP4K3,intron_variant,,ENST00000429397,;MAP4K3,intron_variant,,ENST00000437968,; T ENSG00000011566 ENST00000263881 Transcript intron_variant -/4362 -/2685 -/894 rs113384156 1 -1 MAP4K3 HGNC HGNC:6865 protein_coding YES CCDS1803.1 ENSP00000263881 Q8IVH8 UPI00000747E6 NM_003618.3 1/33 MODIFIER 1 SNV 1 . TCT . . CNRIP1 0 . GRCh38 chr2 68306124 68306124 + Intron SNP C C A novel TUMOR NORMAL C C c.330+11033N>T ENST00000263655 8 6 2 8 8 0 CNRIP1,intron_variant,,ENST00000263655,NM_015463.2;CNRIP1,intron_variant,,ENST00000409559,NM_001111101.1;CNRIP1,intron_variant,,ENST00000481714,; A ENSG00000119865 ENST00000263655 Transcript intron_variant -/1953 -/495 -/164 1 -1 CNRIP1 HGNC HGNC:24546 protein_coding YES CCDS1886.1 ENSP00000263655 Q96F85 UPI0000070FBE NM_015463.2 2/2 MODIFIER 1 SNV 1 . ACA . . RGPD1 0 . GRCh38 chr2 86942193 86942193 + Intron SNP T T G rs202230148 TUMOR NORMAL T T c.49-9103N>G ENST00000559485 771 514 256 279 225 54 RGPD1,intron_variant,,ENST00000559485,NM_001024457.3;RGPD1,intron_variant,,ENST00000409776,;RGPD1,intron_variant,,ENST00000398193,;,regulatory_region_variant,,ENSR00000119786,; G ENSG00000187627 ENST00000559485 Transcript intron_variant -/6697 -/5247 -/1748 rs202230148 1 1 RGPD1 HGNC HGNC:32414 protein_coding YES CCDS46358.2 ENSP00000453170 P0DJD0 UPI00018815D1 NM_001024457.3 1/22 G:0.2778 G:0.0734 G:0.1988 G:0.4593 G:0.3161 G:0.3834 MODIFIER 1 SNV 1 . CTG . . RGPD1 0 . GRCh38 chr2 86942348 86942348 + Intron SNP C C G rs564118497 TUMOR NORMAL C C c.49-8948N>G ENST00000559485 265 187 78 141 112 29 RGPD1,intron_variant,,ENST00000559485,NM_001024457.3;RGPD1,intron_variant,,ENST00000409776,;RGPD1,intron_variant,,ENST00000398193,;,regulatory_region_variant,,ENSR00000119786,; G ENSG00000187627 ENST00000559485 Transcript intron_variant -/6697 -/5247 -/1748 rs564118497 1 1 RGPD1 HGNC HGNC:32414 protein_coding YES CCDS46358.2 ENSP00000453170 P0DJD0 UPI00018815D1 NM_001024457.3 1/22 G:0.2756 MODIFIER 1 SNV 1 . CCG . . RGPD1 0 . GRCh38 chr2 86942392 86942392 + Intron SNP C C G novel TUMOR NORMAL C C c.49-8904N>G ENST00000559485 41 32 9 21 16 5 RGPD1,intron_variant,,ENST00000559485,NM_001024457.3;RGPD1,intron_variant,,ENST00000409776,;RGPD1,intron_variant,,ENST00000398193,;,regulatory_region_variant,,ENSR00000119786,; G ENSG00000187627 ENST00000559485 Transcript intron_variant -/6697 -/5247 -/1748 1 1 RGPD1 HGNC HGNC:32414 protein_coding YES CCDS46358.2 ENSP00000453170 P0DJD0 UPI00018815D1 NM_001024457.3 1/22 MODIFIER 1 SNV 1 . CCG . . RP4-614C10.3 0 . GRCh38 chr2 89625699 89625699 + Intron SNP G G A novel TUMOR NORMAL G G n.869+9N>T ENST00000636037 393 217 176 201 154 47 RP4-614C10.3,intron_variant,,ENST00000636037,; A ENSG00000283132 ENST00000636037 Transcript intron_variant,non_coding_transcript_variant -/1257 1 -1 RP4-614C10.3 Clone_based_vega_gene unprocessed_pseudogene YES 6/8 MODIFIER 1 SNV . AGC . .