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 COSMIC_Codon COSMIC_Gene Transcript_Id Exon ChromChange AAChange Genome_Plus_Minus_10_Bp Drug_Target TTotCov TVarCov NTotCov NVarCov dbSNPPopFreq COSMIC_Gene_Freq COSMIC_Site_Freq TVarRat NVarRat dbSNP_Strength dbSNP_AF dbSNP_PopFreq Confidence Algorithm KIAA1522 57648 hgsc.bcm.edu hg19 1 33236795 33236795 + Missense_Mutation SNP C C A novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . KIAA1522 NM_020888 exon6 c.C2015A p.P672Q TCTCCCCACCTCC . 141.0 46.0 134.0 0.0 . 68 . . . none . . PASS Atlas-SNP SLC5A9 200010 hgsc.bcm.edu hg19 1 48708165 48708165 + Missense_Mutation SNP C C T novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . SLC5A9 NM_001135181 exon14 c.C1789T p.L597F TGCCCCCTCTCTG . 162.0 9.0 129.0 0.0 . 82 . . . none . . PASS Atlas-SNP CTH 1491 hgsc.bcm.edu hg19 1 70895506 70895506 + Silent SNP T T C novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . CTH NM_001902 exon6 c.T618C p.S206S TATTTCTATGTAT . 79.0 26.0 76.0 0.0 . 48 . . . none . . PASS Atlas-SNP ABCA4 24 hgsc.bcm.edu hg19 1 94528186 94528186 + Silent SNP A A T novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . ABCA4 NM_000350 exon13 c.T1884A p.A628A AACTGGAGCCTCC . 59.0 16.0 63.0 0.0 . 275 . . . none . . PASS Atlas-SNP SEMA6C 10500 hgsc.bcm.edu hg19 1 151112138 151112138 + Silent SNP T T C rs200312578 alternate_allele TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . SEMA6C NM_001178061 exon5 c.A273G p.E91E CTCCCCTTCTTCT . 62.0 4.0 50.0 0.0 . 70 . . . alt T|0.999;G|0.001 . PASS Atlas-SNP ADD2 119 hgsc.bcm.edu hg19 2 70900055 70900055 + Missense_Mutation SNP C C A rs138503054 alternate_allele TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . ADD2 NM_017488 exon16 c.G1911T p.R637S TCTCTGCCTCCTT . 52.0 17.0 41.0 0.0 . 261 . . . alt C|1.000;T|0.000 . PASS Atlas-SNP PLEKHB2 55041 hgsc.bcm.edu hg19 2 131904284 131904284 + Missense_Mutation SNP C C G novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . PLEKHB2 NM_001267062 exon9 c.C649G p.L217V CTGGCACTGGGCA . 310.0 84.0 305.0 0.0 . 47 . . . none . . PASS Atlas-SNP HTR2B 3357 hgsc.bcm.edu hg19 2 231988374 231988374 + Missense_Mutation SNP C C A novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . HTR2B NM_000867 exon2 c.G105T p.Q35H TTCTGTCTGTAAT . 144.0 48.0 132.0 0.0 . 33 . . . none . . PASS Atlas-SNP CRTAP 10491 hgsc.bcm.edu hg19 3 33156008 33156008 + Missense_Mutation SNP C C T novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . CRTAP NM_006371 exon1 c.C439T p.P147S CGCGAGCCCTACA . 42.0 14.0 20.0 0.0 . 16 . . . none . . PASS Atlas-SNP USP19 10869 hgsc.bcm.edu hg19 3 49148708 49148708 + Missense_Mutation SNP T T A novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . USP19 NM_001199161 exon22 c.A3308T p.E1103V CGCTGCTCTCGGT . 117.0 58.0 87.0 0.0 . 158 . . . none . . PASS Atlas-SNP USP19 10869 hgsc.bcm.edu hg19 3 49148709 49148709 + Missense_Mutation SNP C C T novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . USP19 NM_001199161 exon22 c.G3307A p.E1103K GCTGCTCTCGGTT . 115.0 58.0 88.0 0.0 . 158 . . . none . . PASS Atlas-SNP DZIP1L 199221 hgsc.bcm.edu hg19 3 137805834 137805834 + Missense_Mutation SNP A A G novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . DZIP1L NM_001170538 exon8 c.T1031C p.L344P TCATGCAGTTCCT . 133.0 31.0 102.0 0.0 . 88 . . . none . . PASS Atlas-SNP EIF4G1 1981 hgsc.bcm.edu hg19 3 184041746 184041746 + Missense_Mutation SNP T T C novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . EIF4G1 NM_001194946 exon17 c.T2474C p.M825T CCAACATGTGCCG . 124.0 33.0 104.0 0.0 . 151 . . . none . . PASS Atlas-SNP LAP3 51056 hgsc.bcm.edu hg19 4 17590497 17590497 + Missense_Mutation SNP G G A novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . LAP3 NM_015907 exon7 c.G760A p.G254R GCCAAAGGATCTG . 134.0 50.0 121.0 0.0 . 50 . . . none . . PASS Atlas-SNP PRKG2 5593 hgsc.bcm.edu hg19 4 82074809 82074809 + Missense_Mutation SNP C C A novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . PRKG2 NM_006259 exon6 c.G979T p.A327S CTTTTGCCAAAAT . 55.0 10.0 57.0 0.0 . 195 . . . none . . PASS Atlas-SNP OSTC 58505 hgsc.bcm.edu hg19 4 109571838 109571838 + Silent SNP C C T novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c OSTC,NS,carcinoma,0,1 OSTC NM_001267818 exon1 c.C27T p.F9F CCCGTTCTTAGTG . 131.0 42.0 90.0 0.0 . 9 . . . none . . PASS Atlas-SNP NDUFS6 4726 hgsc.bcm.edu hg19 5 1801592 1801592 + Missense_Mutation SNP C C A novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . NDUFS6 NM_004553 exon1 c.C61A p.L21M CGGAGCCTGCCCC . 44.0 21.0 32.0 0.0 . 11 . . . none . . PASS Atlas-SNP C6orf195 154386 hgsc.bcm.edu hg19 6 2623684 2623684 + Nonsense_Mutation SNP C C A novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . C6orf195 NM_152554 exon3 c.G373T p.E125X AAGCTTCATTGCT . 75.0 27.0 64.0 0.0 . 10 . . . none . . PASS Atlas-SNP C6orf223 221416 hgsc.bcm.edu hg19 6 43970795 43970795 + Missense_Mutation SNP C C T novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . C6orf223 NM_153246 exon4 c.C661T p.R221C CTAATGCGCTCTA . 88.0 37.0 88.0 0.0 . 14 . . . none . . PASS Atlas-SNP KIAA1919 91749 hgsc.bcm.edu hg19 6 111587895 111587895 + Missense_Mutation SNP A A T novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . KIAA1919 NM_153369 exon4 c.A1130T p.Q377L TTCTTCAAGGAAA . 220.0 67.0 205.0 0.0 . 54 . . . none . . PASS Atlas-SNP THBS2 7058 hgsc.bcm.edu hg19 6 169622311 169622311 + Missense_Mutation SNP G G T novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c THBS2,NS,carcinoma,+1,1 THBS2 NM_003247 exon20 c.C3254A p.T1085K TTCCCCGTGTGCC . 102.0 25.0 150.0 0.0 . 230 . . . none . . PASS Atlas-SNP CCM2 83605 hgsc.bcm.edu hg19 7 45104062 45104062 + Missense_Mutation SNP A A G novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . CCM2 NM_001029835 exon4 c.A352G p.R118G TTCCAGAGAGCCC . 75.0 11.0 41.0 0.0 . 42 . . . none . . PASS Atlas-SNP PCLO 27445 hgsc.bcm.edu hg19 7 82532016 82532016 + Silent SNP A A G novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . PCLO NM_014510 exon9 c.T13479C p.P4493P TGCGTGAGGAAAG . 111.0 63.0 89.0 0.0 . 1506 . . . none . . PASS Atlas-SNP CHCHD3 54927 hgsc.bcm.edu hg19 7 132523165 132523165 + Missense_Mutation SNP T T G novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . CHCHD3 NM_017812 exon6 c.A518C p.K173T TTGAACTTTGCTT . 75.0 39.0 69.0 0.0 . 21 . . . none . . PASS Atlas-SNP KCNV1 27012 hgsc.bcm.edu hg19 8 110986410 110986410 + Missense_Mutation SNP C C A novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . KCNV1 NM_014379 exon1 c.G208T p.V70L CCACCACGGCCAG . 15.0 8.0 18.0 0.0 . 101 . . . none . . PASS Atlas-SNP GOLGA2 2801 hgsc.bcm.edu hg19 9 131028577 131028577 + Nonsense_Mutation SNP G G A novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . GOLGA2 NM_004486 exon8 c.C589T p.Q197X CCAACTGATCCGT . 107.0 39.0 124.0 0.0 . 69 . . . none . . PASS Atlas-SNP UBAC1 10422 hgsc.bcm.edu hg19 9 138839743 138839743 + Silent SNP T T C novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . UBAC1 NM_016172 exon4 c.A342G p.Q114Q CTGGTCTTGTTTT . 34.0 15.0 30.0 0.0 . 40 . . . none . . PASS Atlas-SNP OR4C15 81309 hgsc.bcm.edu hg19 11 55322355 55322355 + Missense_Mutation SNP G G C novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . OR4C15 NM_001001920 exon1 c.G573C p.R191S GAACAGGAGGCTC . 175.0 53.0 138.0 0.0 . 145 . . . none . . PASS Atlas-SNP LRIG3 121227 hgsc.bcm.edu hg19 12 59283874 59283874 + Missense_Mutation SNP T T A novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . LRIG3 NM_153377 exon5 c.A563T p.D188V AAATTGTCAAAAT . 257.0 80.0 253.0 0.0 . 120 . . . none . . PASS Atlas-SNP GPC6 10082 hgsc.bcm.edu hg19 13 94482740 94482740 + Missense_Mutation SNP C C G novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . GPC6 NM_005708 exon3 c.C653G p.A218G TTGCTGCCAGGAC . 53.0 18.0 85.0 0.0 . 102 . . . none . . PASS Atlas-SNP RAP2A 5911 hgsc.bcm.edu hg19 13 98086836 98086836 + Missense_Mutation SNP G G A novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . RAP2A NM_021033 exon1 c.G112A p.D38N ATCGAGGACTTCT . 174.0 57.0 149.0 0.0 . 15 . . . none . . PASS Atlas-SNP GPR18 2841 hgsc.bcm.edu hg19 13 99907879 99907879 + Missense_Mutation SNP G G A novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . GPR18 NM_001098200 exon2 c.C248T p.A83V TCTTTTGCATAAT . 69.0 18.0 79.0 0.0 . 23 . . . none . . PASS Atlas-SNP SNX6 58533 hgsc.bcm.edu hg19 14 35062276 35062276 + Silent SNP A A T novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . SNX6 NM_152233 exon8 c.T729A p.S243S TCTATCAGATTTA . 61.0 18.0 96.0 0.0 . 21 . . . none . . PASS Atlas-SNP CLEC14A 161198 hgsc.bcm.edu hg19 14 38724316 38724316 + Silent SNP C C T novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . CLEC14A NM_175060 exon1 c.G912A p.R304R CGGGCGCCTGGTG . 139.0 50.0 135.0 0.0 . 83 . . . none . . PASS Atlas-SNP FERMT2 10979 hgsc.bcm.edu hg19 14 53386065 53386065 + Missense_Mutation SNP T T A novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . FERMT2 NM_001135000 exon3 c.A167T p.K56I CAATCTTTTTTTA . 99.0 27.0 107.0 0.0 . 59 . . . none . . PASS Atlas-SNP DYNC1H1 1778 hgsc.bcm.edu hg19 14 102466716 102466716 + Missense_Mutation SNP G G A novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . DYNC1H1 NM_001376 exon18 c.G4054A p.V1352I CCCTGGGTTTCAG . 87.0 28.0 85.0 0.0 . 395 . . . none . . PASS Atlas-SNP ATP10A 57194 hgsc.bcm.edu hg19 15 25924510 25924510 + Missense_Mutation SNP G G A novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . ATP10A NM_024490 exon21 c.C4478T p.A1493V GAAGATGCTCCTA . 100.0 25.0 74.0 0.0 . 270 . . . none . . PASS Atlas-SNP ZNF598 90850 hgsc.bcm.edu hg19 16 2052644 2052644 + Silent SNP C C T novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . ZNF598 NM_178167 exon6 c.G555A p.G185G CGGGTGCCCACGG . 50.0 10.0 40.0 0.0 . 55 . . . none . . PASS Atlas-SNP CLUAP1 23059 hgsc.bcm.edu hg19 16 3554721 3554721 + Silent SNP T T C novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . CLUAP1 NM_015041 exon2 c.T24C p.N8N GACAGATTTCACA . 105.0 21.0 60.0 0.0 . 32 . . . none . . PASS Atlas-SNP TIAF1 9220 hgsc.bcm.edu hg19 17 27400954 27400954 + Missense_Mutation SNP C C G novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . TIAF1 NM_004740 exon1 c.G264C p.R88S ATCAGCCCTGAAC . 251.0 129.0 206.0 0.0 . 9 . . . none . . PASS Atlas-SNP TMEM101 84336 hgsc.bcm.edu hg19 17 42089524 42089524 + Silent SNP C C T novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . TMEM101 NM_032376 exon4 c.G546A p.L182L GAAGAACAGCTGG . 122.0 27.0 97.0 0.0 . 18 . . . none . . PASS Atlas-SNP BZRAP1 9256 hgsc.bcm.edu hg19 17 56386306 56386306 + Missense_Mutation SNP G G T novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . BZRAP1 NM_004758 exon22 c.C4327A p.L1443M GGCCCAGTCGTCC . 149.0 36.0 89.0 0.0 . 287 . . . none . . PASS Atlas-SNP KCNH6 81033 hgsc.bcm.edu hg19 17 61623123 61623123 + Silent SNP C C T novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c KCNH6,bladder,carcinoma,0,2 KCNH6 NM_030779 exon14 c.C2845T p.L949L TCACCTCTACATC . 169.0 33.0 126.0 0.0 . 122 . . . none . . PASS Atlas-SNP THOC1 9984 hgsc.bcm.edu hg19 18 214909 214909 + Missense_Mutation SNP C C A novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . THOC1 NM_005131 exon21 c.G1691T p.R564L TCTCGCCGAACAT . 171.0 8.0 157.0 0.0 . 43 . . . none . . PASS Atlas-SNP ANKRD12 23253 hgsc.bcm.edu hg19 18 9257291 9257291 + Silent SNP T T C novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . ANKRD12 NM_015208 exon9 c.T4026C p.T1342T AGATACTAGTCCT . 120.0 43.0 132.0 0.0 . 167 . . . none . . PASS Atlas-SNP ASXL3 80816 hgsc.bcm.edu hg19 18 31263418 31263418 + Silent SNP A A G novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . ASXL3 NM_030632 exon8 c.A765G p.G255G CCCAGGATCTATT . 54.0 14.0 53.0 0.0 . 405 . . . none . . PASS Atlas-SNP ELAC1 55520 hgsc.bcm.edu hg19 18 48513160 48513160 + Missense_Mutation SNP G G C novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . ELAC1 NM_018696 exon4 c.G797C p.C266S AACTGTGCTTTGA . 48.0 14.0 55.0 0.0 . 17 . . . none . . PASS Atlas-SNP ZNF763 284390 hgsc.bcm.edu hg19 19 12089881 12089881 + Missense_Mutation SNP T T C novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . ZNF763 NM_001012753 exon4 c.T1151C p.F384S ATAAGTTTTCAAA . 143.0 55.0 121.0 0.0 . 31 . . . none . . PASS Atlas-SNP ZSWIM4 65249 hgsc.bcm.edu hg19 19 13915960 13915960 + Missense_Mutation SNP A A G novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . ZSWIM4 NM_023072 exon3 c.A710G p.N237S TGGTGAATGGTAA . 64.0 17.0 73.0 0.0 . 69 . . . none . . PASS Atlas-SNP JAK3 3718 hgsc.bcm.edu hg19 19 17946018 17946018 + Missense_Mutation SNP T T C novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . JAK3 NM_000215 exon15 c.A1921G p.K641E GGCCTTTGTCCTC . 50.0 13.0 52.0 0.0 . 341 . . . none . . PASS Atlas-SNP ZNF566 84924 hgsc.bcm.edu hg19 19 36940231 36940231 + Missense_Mutation SNP T T C novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . ZNF566 NM_001145343 exon5 c.A908G p.Q303R ATTCTCTGATGTT . 119.0 5.0 92.0 0.0 . 40 . . . none . . PASS Atlas-SNP ZNF787 126208 hgsc.bcm.edu hg19 19 56599455 56599455 + Missense_Mutation SNP C C G rs202243737 TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . ZNF787 NM_001002836 exon3 c.G1086C p.E362D GTCGTCCTCCTCC . 26.0 14.0 11.0 0.0 . 20 . . . weak C|0.996;G|0.004 0.004 PASS Atlas-SNP SALL4 57167 hgsc.bcm.edu hg19 20 50405586 50405586 + Silent SNP G G A novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . SALL4 NM_020436 exon3 c.C2556T p.S852S CCCTGGGGACAAT . 59.0 19.0 73.0 0.0 . 168 . . . none . . PASS Atlas-SNP KRTAP13-1 140258 hgsc.bcm.edu hg19 21 31768620 31768620 + Missense_Mutation SNP G G T novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . KRTAP13-1 NM_181599 exon1 c.G216T p.E72D TGTGGAGTCCAGC . 83.0 26.0 89.0 0.0 . 48 . . . none . . PASS Atlas-SNP NDUFV3 4731 hgsc.bcm.edu hg19 21 44317078 44317078 + Silent SNP T T C novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . NDUFV3 NM_001001503 exon2 c.T90C p.S30S TGCTTCTACGGTT . 94.0 27.0 121.0 0.0 . 23 . . . none . . PASS Atlas-SNP PPM1F 9647 hgsc.bcm.edu hg19 22 22287929 22287929 + Missense_Mutation SNP A A G novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . PPM1F NM_014634 exon5 c.T581C p.F194S ACAGCAAAGTAGG . 57.0 25.0 47.0 0.0 . 34 . . . none . . PASS Atlas-SNP SFI1 9814 hgsc.bcm.edu hg19 22 31924806 31924806 + Missense_Mutation SNP C C T novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . SFI1 NM_001007467 exon3 c.C223T p.H75Y GGCACACATACTT . 130.0 41.0 110.0 0.0 . 78 . . . none . . PASS Atlas-SNP APOL1 8542 hgsc.bcm.edu hg19 22 36661665 36661665 + Silent SNP C C T novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . APOL1 NM_145343 exon7 c.C831T p.N277N TGAGAACATATCC . 60.0 18.0 66.0 0.0 . 35 . . . none . . PASS Atlas-SNP RPL10 6134 hgsc.bcm.edu hg19 X 153627911 153627911 + Missense_Mutation SNP G G A novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . RPL10 NM_001256577 exon4 c.G166A p.E56K TCAGATGAATATG . 89.0 50.0 91.0 0.0 . 22 . . . none . . PASS Atlas-SNP MITF 4286 hgsc.bcm.edu hg19 3 69988260 69988261 + Frame_Shift_Ins INS - - T novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c MITF,rectum,carcinoma,0,1 MITF NM_198159 exon4 c.594_595insT p.K198fs . . 75.0 38.0 47.0 0.0 . 156 . 0.506667 0 none . . PASS Atlas-INDEL KDR 3791 hgsc.bcm.edu hg19 4 55981041 55981042 + Frame_Shift_Ins INS - - T novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . KDR NM_002253 exon5 c.658_659insA p.G220fs . . 93.0 27.0 83.0 0.0 . 307 . 0.290323 0 none . . PASS Atlas-INDEL PROX1 5629 hgsc.bcm.edu hg19 1 214170437 214170438 + Frame_Shift_Ins INS - - AT novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . PROX1 NM_001270616 exon2 c.559_560insAT p.N187fs . . 74.0 21.0 79.0 0.0 . 124 . 0.283784 0 none . . PASS Atlas-INDEL C2CD3 26005 hgsc.bcm.edu hg19 11 73745646 73745646 + Frame_Shift_Del DEL G G - novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . C2CD3 NM_015531 exon31 c.5890delT p.X1964E . . 40.0 10.0 51.0 0.0 . 288 . 0.25 0 none . . PASS Atlas-INDEL PLEKHB2 55041 hgsc.bcm.edu hg19 2 131904282 131904282 + Frame_Shift_Del DEL C C - novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . PLEKHB2 NM_001267062 exon9 c.646delG p.A216fs . . 311.0 83.0 293.0 0.0 . 47 . 0.266881 0 none . . PASS Atlas-INDEL GFRAL 389400 hgsc.bcm.edu hg19 6 55223709 55223709 + Frame_Shift_Del DEL C C - novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . GFRAL NM_207410 exon6 c.724delT p.S242fs . . 130.0 46.0 112.0 0.0 . 91 . 0.353846 0 none . . PASS Atlas-INDEL HAPLN3 145864 hgsc.bcm.edu hg19 15 89422488 89422488 + Frame_Shift_Del DEL G G - novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . HAPLN3 NM_178232 exon4 c.507delT p.P169fs . . 65.0 19.0 68.0 0.0 . 43 . 0.292308 0 none . . PASS Atlas-INDEL DNAJC28 54943 hgsc.bcm.edu hg19 21 34861049 34861050 + Frame_Shift_Ins INS - - A novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c DNAJC28,right_lower_lobe,carcinoma,0,1 DNAJC28 NM_001040192 exon2 c.652_653insT p.D218_N219delinsX . . 202.0 51.0 202.0 0.0 . 47 . 0.252475 0 none . . PASS Atlas-INDEL CISH 1154 hgsc.bcm.edu hg19 3 50645554 50645554 + Frame_Shift_Del DEL A A - novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . CISH NM_013324 exon4 c.313delA p.T105fs . . 71.0 10.0 67.0 0.0 . 27 . 0.140845 0 none . . PASS Atlas-INDEL AZI2 64343 hgsc.bcm.edu hg19 3 28382066 28382066 + Frame_Shift_Del DEL C C - novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . AZI2 NM_001134432 exon2 c.44delA p.E15fs . . 127.0 50.0 121.0 0.0 . 33 . 0.393701 0 none . . PASS Atlas-INDEL KIAA1211 57482 hgsc.bcm.edu hg19 4 57182080 57182080 + Frame_Shift_Del DEL T T - novel TCGA-BQ-7045-01A-31D-1961-08 TCGA-BQ-7045-11A-01D-1961-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 413a9e10-cac7-4b6c-91cd-b58fd4499c07 0ed1c015-2f52-4269-98d4-b78e9323f29c . KIAA1211 NM_020722 exon8 c.2411delC p.P804fs . . 65.0 22.0 94.0 0.0 . 178 . 0.338462 0 none . . PASS Atlas-INDEL