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 EBNA1BP2 10969 hgsc.bcm.edu hg19 1 43637311 43637311 + Silent SNP C C T novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . EBNA1BP2 NM_001159936 exon4 c.G327A p.K109K ACATTGCTTCAGG . 101.0 37.0 75.0 0.0 . 37 . . . none . . PASS Atlas-SNP NRD1 4898 hgsc.bcm.edu hg19 1 52277743 52277743 + Missense_Mutation SNP T T C novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . NRD1 NM_002525 exon17 c.A1906G p.M636V CACACATGTTTTC . 89.0 31.0 85.0 0.0 . 89 . . . none . . PASS Atlas-SNP LRRC8D 55144 hgsc.bcm.edu hg19 1 90399387 90399387 + Missense_Mutation SNP A A C novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . LRRC8D NM_018103 exon3 c.A760C p.I254L CCAATGATCAATA . 52.0 20.0 48.0 0.0 . 78 . . . none . . PASS Atlas-SNP PTBP2 58155 hgsc.bcm.edu hg19 1 97278858 97278858 + Missense_Mutation SNP T T C novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . PTBP2 NM_021190 exon14 c.T1493C p.M498T TTCAGATGGCAAC . 247.0 79.0 251.0 0.0 . 62 . . . none . . PASS Atlas-SNP MAGI3 260425 hgsc.bcm.edu hg19 1 114184618 114184618 + Silent SNP C C T novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . MAGI3 NM_152900 exon10 c.C1446T p.V482V ACCTGTCAATCAG . 79.0 29.0 69.0 0.0 . 181 . . . none . . PASS Atlas-SNP ITGA10 8515 hgsc.bcm.edu hg19 1 145525111 145525111 + Missense_Mutation SNP C C A novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . ITGA10 NM_003637 exon1 c.C46A p.L16M GTGTTCCTGACAG . 109.0 24.0 105.0 0.0 . 131 . . . none . . PASS Atlas-SNP SNX27 81609 hgsc.bcm.edu hg19 1 151611491 151611491 + Missense_Mutation SNP G G C novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . SNX27 NM_030918 exon2 c.G439C p.D147H CCCAGTGACGACT . 84.0 30.0 62.0 0.0 . 44 . . . none . . PASS Atlas-SNP TDRD10 126668 hgsc.bcm.edu hg19 1 154520167 154520167 + Missense_Mutation SNP A A T novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . TDRD10 NM_182499 exon13 c.A1037T p.K346M TCCTAAAGTTTGA . 173.0 68.0 148.0 0.0 . 48 . . . none . . PASS Atlas-SNP SLC30A1 7779 hgsc.bcm.edu hg19 1 211751453 211751453 + Missense_Mutation SNP T T C novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . SLC30A1 NM_021194 exon1 c.A502G p.T168A GGCGGGTGCTCTT . 43.0 18.0 34.0 0.0 . 27 . . . none . . PASS Atlas-SNP NSL1 25936 hgsc.bcm.edu hg19 1 212960912 212960912 + Missense_Mutation SNP T T C novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . NSL1 NM_015471 exon2 c.A302G p.N101S AAACAATTATCTG . 272.0 92.0 219.0 0.0 . 24 . . . none . . PASS Atlas-SNP OR2L5 81466 hgsc.bcm.edu hg19 1 248186098 248186098 + Missense_Mutation SNP G G T novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . . NM_001258284 exon1 c.G849T p.M283I CCCAATGCTCAAC . 62.0 19.0 53.0 0.0 . . . . . none . . PASS Atlas-SNP GRHL1 29841 hgsc.bcm.edu hg19 2 10140748 10140748 + Silent SNP T T C novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . GRHL1 NM_198182 exon16 c.T1770C p.I590I CAACATTGTGAAG . 52.0 22.0 45.0 0.0 . 95 . . . none . . PASS Atlas-SNP NBAS 51594 hgsc.bcm.edu hg19 2 15415752 15415752 + Silent SNP A A T novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 NBAS,rectum,NS,0,1 NBAS NM_015909 exon44 c.T5580A p.P1860P GAGATGAGGGTCT . 93.0 43.0 84.0 1.0 . 246 . . . none . . PASS Atlas-SNP SMC6 79677 hgsc.bcm.edu hg19 2 17881504 17881504 + Nonsense_Mutation SNP G G A novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . SMC6 NM_001142286 exon21 c.C2365T p.Q789X ATAGTTGATTAAT . 290.0 123.0 279.0 1.0 . 102 . . . none . . PASS Atlas-SNP SRBD1 55133 hgsc.bcm.edu hg19 2 45645662 45645662 + Missense_Mutation SNP A A C novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . SRBD1 NM_018079 exon18 c.T2175G p.N725K GTTGGCATTGAGT . 140.0 54.0 93.0 0.0 . 107 . . . none . . PASS Atlas-SNP SPTBN1 6711 hgsc.bcm.edu hg19 2 54874386 54874386 + Missense_Mutation SNP G G C rs200274009 by1000genomes;alternate_allele TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . SPTBN1 NM_003128 exon24 c.G4985C p.S1662T CCGACAGCCATCC . 31.0 14.0 23.0 0.0 . 378 . . . alt G|1.000;A|0.000 . PASS Atlas-SNP ITGA6 3655 hgsc.bcm.edu hg19 2 173349951 173349951 + Missense_Mutation SNP C C T novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . ITGA6 NM_000210 exon13 c.C1813T p.P605S GTTCTTCCAATTC . 157.0 68.0 154.0 0.0 . 171 . . . none . . PASS Atlas-SNP NAB1 4664 hgsc.bcm.edu hg19 2 191524460 191524460 + Missense_Mutation SNP G G T novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . NAB1 NM_005966 exon4 c.G558T p.E186D AAAGGAGAGCAGT . 77.0 33.0 79.0 0.0 . 31 . . . none . . PASS Atlas-SNP TMBIM1 64114 hgsc.bcm.edu hg19 2 219140208 219140208 + Missense_Mutation SNP T T C novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . TMBIM1 NM_022152 exon12 c.A926G p.D309G TTGCGATCCCCCA . 36.0 14.0 25.0 0.0 . 20 . . . none . . PASS Atlas-SNP TRIP12 9320 hgsc.bcm.edu hg19 2 230659907 230659907 + Missense_Mutation SNP C C T novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . TRIP12 NM_004238 exon25 c.G3731A p.G1244E CCTGTCCCATTTC . 55.0 16.0 71.0 0.0 . 207 . . . none . . PASS Atlas-SNP KLHL30 377007 hgsc.bcm.edu hg19 2 239057702 239057702 + Missense_Mutation SNP G G C novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 KLHL30_ENST00000409223,right_upper_lobe,carcinoma,0,2 KLHL30 NM_198582 exon7 c.G1394C p.R465P CGCCTCGCTGTGC . 29.0 13.0 15.0 0.0 . 79 . . . none . . PASS Atlas-SNP XYLB 9942 hgsc.bcm.edu hg19 3 38408332 38408332 + Missense_Mutation SNP C C A novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . XYLB NM_005108 exon7 c.C541A p.Q181K ATTTACCAGCAGA . 61.0 22.0 32.0 0.0 . 50 . . . none . . PASS Atlas-SNP QRICH1 54870 hgsc.bcm.edu hg19 3 49114324 49114324 + Nonsense_Mutation SNP G G A novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . QRICH1 NM_198880 exon2 c.C127T p.Q43X ACTCCTGAAGGGC . 87.0 34.0 75.0 0.0 . 48 . . . none . . PASS Atlas-SNP CHST13 166012 hgsc.bcm.edu hg19 3 126260730 126260730 + Missense_Mutation SNP T T C novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . CHST13 NM_152889 exon3 c.T335C p.V112A GCTACGTGCCCAA . 67.0 22.0 108.0 0.0 . 21 . . . none . . PASS Atlas-SNP WDFY3 23001 hgsc.bcm.edu hg19 4 85758174 85758174 + Missense_Mutation SNP C C G novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . WDFY3 NM_014991 exon7 c.G484C p.D162H GAAGGTCAAAAAA . 239.0 88.0 213.0 0.0 . 314 . . . none . . PASS Atlas-SNP FHDC1 85462 hgsc.bcm.edu hg19 4 153897841 153897841 + Missense_Mutation SNP C C T novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . FHDC1 NM_033393 exon11 c.C3398T p.T1133M GGACCACGCTGGG . 38.0 14.0 39.0 0.0 . 102 . . . none . . PASS Atlas-SNP IQGAP2 10788 hgsc.bcm.edu hg19 5 75970433 75970433 + Silent SNP C C T novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . IQGAP2 NM_006633 exon27 c.C3426T p.A1142A AGTGGCCAAGGTT . 99.0 37.0 78.0 0.0 . 186 . . . none . . PASS Atlas-SNP FEM1C 56929 hgsc.bcm.edu hg19 5 114860103 114860103 + Silent SNP A A G novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . FEM1C NM_020177 exon3 c.T1756C p.L586L ACTGCAATGTGGT . 147.0 57.0 102.0 0.0 . 50 . . . none . . PASS Atlas-SNP PCDHA13 56136 hgsc.bcm.edu hg19 5 140263609 140263609 + Missense_Mutation SNP G G T novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 PCDHA13,NS,carcinoma,0,1 PCDHA13 NM_031865 exon1 c.G1756T p.G586C TCGGTGGGTGCAG . 59.0 20.0 54.0 0.0 . 213 . . . none . . PASS Atlas-SNP CLK4 57396 hgsc.bcm.edu hg19 5 178045754 178045754 + Missense_Mutation SNP T T C novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . CLK4 NM_020666 exon3 c.A187G p.N63D GCTCATTCAAGGA . 65.0 26.0 67.0 0.0 . 103 . . . none . . PASS Atlas-SNP SLC22A7 10864 hgsc.bcm.edu hg19 6 43269967 43269967 + Missense_Mutation SNP T T C novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . SLC22A7 NM_153320 exon7 c.T1091C p.L364P ACGGCCTGAGTCT . 56.0 18.0 50.0 0.0 . 69 . . . none . . PASS Atlas-SNP PKHD1 5314 hgsc.bcm.edu hg19 6 51924726 51924726 + Missense_Mutation SNP C C A novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . PKHD1 NM_170724 exon15 c.G1233T p.K411N GAATACCTTAGTC . 33.0 8.0 33.0 0.0 . 927 . . . none . . PASS Atlas-SNP SMAP1 60682 hgsc.bcm.edu hg19 6 71377783 71377783 + Silent SNP C C A novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 SMAP1_ENST00000370455,NS,carcinoma,0,2 SMAP1 NM_001044305 exon1 c.C57A p.L19L CCAGCTCATCCTA . 81.0 35.0 71.0 0.0 . 77 . . . none . . PASS Atlas-SNP EEF1A1 1915 hgsc.bcm.edu hg19 6 74228567 74228567 + Missense_Mutation SNP G G T novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . EEF1A1 NM_001402 exon5 c.C626A p.P209H AACCAAGGCATCT . 85.0 38.0 86.0 0.0 . 56 . . . none . . PASS Atlas-SNP QRSL1 55278 hgsc.bcm.edu hg19 6 107111042 107111042 + Missense_Mutation SNP C C A novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . QRSL1 NM_018292 exon10 c.C1348A p.Q450K TTTACACAAGCTG . 59.0 13.0 57.0 0.0 . 30 . . . none . . PASS Atlas-SNP RAET1E 135250 hgsc.bcm.edu hg19 6 150211134 150211134 + Missense_Mutation SNP C C T novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . RAET1E NM_139165 exon2 c.G233A p.G78E TTCTTCCCCAGGA . 133.0 45.0 100.0 0.0 . 20 . . . none . . PASS Atlas-SNP MLXIPL 51085 hgsc.bcm.edu hg19 7 73038696 73038696 + Missense_Mutation SNP G G A novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . MLXIPL NM_032954 exon1 c.C127T p.R43C GCGAGCGGAGCAA . 49.0 20.0 20.0 0.0 . 54 . . . none . . PASS Atlas-SNP TRRAP 8295 hgsc.bcm.edu hg19 7 98506430 98506430 + Missense_Mutation SNP G G C novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 TRRAP_ENST00000359863,NS,carcinoma,0,4 TRRAP NM_001244580 exon14 c.G1195C p.V399L CTCGCCGTCCAGC . 97.0 42.0 49.0 0.0 . 863 . . . none . . PASS Atlas-SNP ZKSCAN5 23660 hgsc.bcm.edu hg19 7 99117529 99117529 + Silent SNP C C T novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . ZKSCAN5 NM_145102 exon4 c.C633T p.S211S TGGGTCCCAGGTG . 67.0 35.0 39.0 0.0 . 63 . . . none . . PASS Atlas-SNP ZNF282 8427 hgsc.bcm.edu hg19 7 148892698 148892698 + Missense_Mutation SNP C C A novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . ZNF282 NM_003575 exon1 c.C17A p.T6K TGTCAACACGGCC . 54.0 22.0 27.0 0.0 . 42 . . . none . . PASS Atlas-SNP RP1 6101 hgsc.bcm.edu hg19 8 55537660 55537660 + Silent SNP G G A novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 RP1,colon,carcinoma,0,1 RP1 NM_006269 exon4 c.G1218A p.E406E GGCAGAGGAGATA . 93.0 35.0 86.0 0.0 . 429 . . . none . . PASS Atlas-SNP ARFGEF1 10565 hgsc.bcm.edu hg19 8 68200291 68200291 + Missense_Mutation SNP T T C novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . ARFGEF1 NM_006421 exon7 c.A926G p.K309R TCATTTTTAGATA . 101.0 38.0 82.0 0.0 . 196 . . . none . . PASS Atlas-SNP CLTA 1211 hgsc.bcm.edu hg19 9 36204095 36204095 + Nonsense_Mutation SNP G G A novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . CLTA NM_001184761 exon4 c.G404A p.W135X CAGAGTGGAAAGA . 66.0 21.0 59.0 0.0 . 18 . . . none . . PASS Atlas-SNP KIF27 55582 hgsc.bcm.edu hg19 9 86518501 86518501 + Missense_Mutation SNP T T C novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . KIF27 NM_017576 exon4 c.A932G p.K311R ACAGTCTTAGCAC . 130.0 49.0 143.0 0.0 . 103 . . . none . . PASS Atlas-SNP ANKS6 203286 hgsc.bcm.edu hg19 9 101498890 101498890 + Missense_Mutation SNP T T G novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . ANKS6 NM_173551 exon15 c.A2527C p.I843L GTAAAATTTGTCT . 59.0 11.0 55.0 0.0 . 59 . . . none . . PASS Atlas-SNP STX17 55014 hgsc.bcm.edu hg19 9 102730737 102730737 + Missense_Mutation SNP G G A novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . STX17 NM_017919 exon8 c.G691A p.A231T CTGGCAGCTCTGC . 61.0 22.0 52.0 0.0 . 17 . . . none . . PASS Atlas-SNP ENTPD8 377841 hgsc.bcm.edu hg19 9 140332422 140332422 + Nonsense_Mutation SNP C C A novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . ENTPD8 NM_198585 exon3 c.G241T p.E81X AACCTTCCACCTG . 20.0 10.0 31.0 0.0 . 53 . . . none . . PASS Atlas-SNP DIP2C 22982 hgsc.bcm.edu hg19 10 375429 375429 + Missense_Mutation SNP A A G novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . DIP2C NM_014974 exon30 c.T3697C p.Y1233H CGGAGTAGGAGCA . 24.0 8.0 35.0 0.0 . 195 . . . none . . PASS Atlas-SNP ASB13 79754 hgsc.bcm.edu hg19 10 5683908 5683908 + Silent SNP C C T novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . ASB13 NM_024701 exon5 c.G534A p.A178A CTTTGCCGCATTC . 84.0 28.0 78.0 0.0 . 26 . . . none . . PASS Atlas-SNP IPMK 253430 hgsc.bcm.edu hg19 10 59986850 59986850 + Silent SNP A A G novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . IPMK NM_152230 exon3 c.T327C p.Y109Y TGGCAAATATTTT . 49.0 15.0 52.0 0.0 . 45 . . . none . . PASS Atlas-SNP CCAR1 55749 hgsc.bcm.edu hg19 10 70547942 70547942 + Missense_Mutation SNP C C T novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . CCAR1 NM_018237 exon23 c.C3044T p.S1015L AGGAATCAAAGGA . 290.0 118.0 241.0 0.0 . 118 . . . none . . PASS Atlas-SNP SEC24C 9632 hgsc.bcm.edu hg19 10 75529171 75529171 + Missense_Mutation SNP T T G novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . SEC24C NM_198597 exon18 c.T2491G p.C831G CTGAACTGCTGCA . 95.0 45.0 85.0 0.0 . 86 . . . none . . PASS Atlas-SNP AFAP1L2 84632 hgsc.bcm.edu hg19 10 116062118 116062118 + Missense_Mutation SNP A A T novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . AFAP1L2 NM_032550 exon12 c.T1410A p.S470R GGCCGCACTCACA . 48.0 4.0 56.0 0.0 . 90 . . . none . . PASS Atlas-SNP BCCIP 56647 hgsc.bcm.edu hg19 10 127515167 127515167 + Missense_Mutation SNP A A T novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . BCCIP NM_016567 exon2 c.A173T p.N58I AAGTGAATATTGA . 78.0 16.0 72.0 0.0 . 48 . . . none . . PASS Atlas-SNP NAV2 89797 hgsc.bcm.edu hg19 11 20065595 20065595 + Silent SNP A A G novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . NAV2 NM_001244963 exon14 c.A3045G p.S1015S GAAATCAGACGGA . 50.0 17.0 33.0 0.0 . 255 . . . none . . PASS Atlas-SNP SLC5A12 159963 hgsc.bcm.edu hg19 11 26720062 26720062 + Missense_Mutation SNP A A G novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . SLC5A12 NM_178498 exon7 c.T842C p.L281P AGACCCAGCAAGT . 76.0 34.0 55.0 0.0 . 134 . . . none . . PASS Atlas-SNP ZNF408 79797 hgsc.bcm.edu hg19 11 46724728 46724728 + Missense_Mutation SNP A A C rs376220307 bycluster TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 ZNF408,caecum,carcinoma,0,1 ZNF408 NM_024741 exon4 c.A587C p.E196A TGACAGAAGTGGA . 37.0 4.0 31.0 0.0 . 70 . . . weak . . PASS Atlas-SNP C11orf73 51501 hgsc.bcm.edu hg19 11 86048421 86048421 + Missense_Mutation SNP G G C novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . C11orf73 NM_016401 exon3 c.G269C p.G90A TTGCAGGAGAAGG . 90.0 32.0 76.0 0.0 . 9 . . . none . . PASS Atlas-SNP ITPR2 3709 hgsc.bcm.edu hg19 12 26810815 26810815 + Missense_Mutation SNP T T C novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . ITPR2 NM_002223 exon18 c.A2017G p.M673V CTTGCATTGAGAC . 132.0 50.0 126.0 0.0 . 270 . . . none . . PASS Atlas-SNP MLL2 8085 hgsc.bcm.edu hg19 12 49445630 49445630 + Silent SNP A A G novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . MLL2 NM_003482 exon10 c.T1836C p.P612P CTCCTCAGGTGGA . 45.0 14.0 39.0 0.0 . 1173 . . . none . . PASS Atlas-SNP KERA 11081 hgsc.bcm.edu hg19 12 91445296 91445296 + Splice_Site SNP C C T novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . KERA NM_007035 exon4 c.887-1G>A . TCACACCTACAGT . 26.0 12.0 23.0 0.0 . 62 . . . none . . PASS Atlas-SNP MTERFD3 80298 hgsc.bcm.edu hg19 12 107371849 107371849 + Missense_Mutation SNP T T A novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . MTERFD3 NM_001033050 exon3 c.A644T p.Q215L GGGTTTTGGCTTA . 102.0 38.0 79.0 0.0 . 32 . . . none . . PASS Atlas-SNP ALDH2 217 hgsc.bcm.edu hg19 12 112220989 112220989 + Missense_Mutation SNP G G A rs375845001 TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . ALDH2 NM_000690 exon3 c.G247A p.A83T AAGGCCGCCCGGG . 36.0 14.0 31.0 0.0 . 91 . . . weak . . PASS Atlas-SNP ALDH2 217 hgsc.bcm.edu hg19 12 112220990 112220990 + Missense_Mutation SNP C C A novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . ALDH2 NM_000690 exon3 c.C248A p.A83D AGGCCGCCCGGGC . 36.0 14.0 32.0 0.0 . 91 . . . none . . PASS Atlas-SNP C12orf43 64897 hgsc.bcm.edu hg19 12 121441960 121441960 + Missense_Mutation SNP T T C novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . C12orf43 NM_022895 exon6 c.A785G p.N262S GTTCAGTTTGCAG . 121.0 38.0 96.0 0.0 . 30 . . . none . . PASS Atlas-SNP KNTC1 9735 hgsc.bcm.edu hg19 12 123089162 123089162 + Nonsense_Mutation SNP G G A novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . KNTC1 NM_014708 exon49 c.G5153A p.W1718X AGAGATGGCTACA . 77.0 23.0 88.0 0.0 . 182 . . . none . . PASS Atlas-SNP KNTC1 9735 hgsc.bcm.edu hg19 12 123089163 123089163 + Missense_Mutation SNP G G T novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . KNTC1 NM_014708 exon49 c.G5154T p.W1718C GAGATGGCTACAG . 77.0 23.0 88.0 0.0 . 182 . . . none . . PASS Atlas-SNP CCDC62 84660 hgsc.bcm.edu hg19 12 123285813 123285813 + Missense_Mutation SNP G G A novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . CCDC62 NM_201435 exon9 c.G1120A p.D374N TCTTGCGATGAAT . 122.0 46.0 101.0 0.0 . 119 . . . none . . PASS Atlas-SNP PCDH20 64881 hgsc.bcm.edu hg19 13 61986120 61986120 + Silent SNP C C T novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 PCDH20_ENST00000409186,NS,carcinoma,0,2 PCDH20 NM_022843 exon2 c.G2112A p.Q704Q GCTTTGCTGCTCT . 85.0 25.0 82.0 0.0 . 265 . . . none . . PASS Atlas-SNP RAB20 55647 hgsc.bcm.edu hg19 13 111213813 111213813 + Missense_Mutation SNP C C G novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . RAB20 NM_017817 exon1 c.G54C p.K18N CGACGTCTTCCCC . 107.0 22.0 61.0 0.0 . 34 . . . none . . PASS Atlas-SNP CEBPE 1053 hgsc.bcm.edu hg19 14 23586764 23586764 + Missense_Mutation SNP G G A novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . CEBPE NM_001805 exon2 c.C778T p.L260F TGCGGAGGGTGTC . 39.0 16.0 36.0 0.0 . 34 . . . none . . PASS Atlas-SNP SDR39U1 56948 hgsc.bcm.edu hg19 14 24911432 24911432 + Missense_Mutation SNP T T C rs201052867 bycluster;alternate_allele TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . SDR39U1 NM_020195 exon3 c.A158G p.D53G GCGGCATCGCAGC . 35.0 17.0 34.0 0.0 . 19 . . . alt . . PASS Atlas-SNP SERPINA3 12 hgsc.bcm.edu hg19 14 95089993 95089993 + Missense_Mutation SNP G G A novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . SERPINA3 NM_001085 exon5 c.G1114A p.A372T ACAGAAGCATCTG . 86.0 24.0 98.0 0.0 . 78 . . . none . . PASS Atlas-SNP SYNE3 161176 hgsc.bcm.edu hg19 14 95942145 95942145 + Missense_Mutation SNP G G A novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . SYNE3 NM_152592 exon1 c.C14T p.P5L TCCTGGGGCTGCT . 32.0 12.0 29.0 0.0 . 130 . . . none . . PASS Atlas-SNP NARG2 79664 hgsc.bcm.edu hg19 15 60741577 60741577 + Missense_Mutation SNP A A T novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . NARG2 NM_024611 exon10 c.T1589A p.M530K ATAGTCATATCAT . 93.0 38.0 87.0 0.0 . 82 . . . none . . PASS Atlas-SNP RORA 6095 hgsc.bcm.edu hg19 15 60803577 60803577 + Missense_Mutation SNP A A G novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . RORA NM_134260 exon6 c.T767C p.L256P ATGTCCAGGTAGA . 207.0 73.0 148.0 0.0 . 114 . . . none . . PASS Atlas-SNP AKAP13 11214 hgsc.bcm.edu hg19 15 86122646 86122646 + Silent SNP C C T novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . AKAP13 NM_007200 exon7 c.C1347T p.D449D GAGAGACTTGGTC . 79.0 31.0 78.0 0.0 . 394 . . . none . . PASS Atlas-SNP HMOX2 3163 hgsc.bcm.edu hg19 16 4557964 4557964 + Missense_Mutation SNP A A G novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . HMOX2 NM_001127205 exon4 c.A455G p.H152R TGGCCCATGCATA . 90.0 41.0 50.0 0.0 . 22 . . . none . . PASS Atlas-SNP CES1 1066 hgsc.bcm.edu hg19 16 55846940 55846940 + Missense_Mutation SNP C C T rs138161688 TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . CES1 NM_001025195 exon9 c.G961A p.G321S CAGTGCCCAGAAG . 48.0 30.0 32.0 0.0 . 78 . . . weak C|1.000;T|0.000 0.000 PASS Atlas-SNP E2F4 1874 hgsc.bcm.edu hg19 16 67226690 67226690 + Silent SNP G G A rs143700278 TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . E2F4 NM_001950 exon2 c.G162A p.Q54Q ACGCCAGAAGCGG . 72.0 37.0 63.0 0.0 . 25 . . . weak G|1.000;A|0.000 0.000 PASS Atlas-SNP AARS 16 hgsc.bcm.edu hg19 16 70316587 70316587 + Missense_Mutation SNP T T C rs77753666 bycluster;alternate_allele TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . AARS NM_001605 exon2 c.A80G p.H27R GACGAGTGAACAT . 100.0 60.0 74.0 0.0 . 62 . . . alt . . PASS Atlas-SNP FAM92B 339145 hgsc.bcm.edu hg19 16 85144008 85144008 + Missense_Mutation SNP G G C novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . FAM92B NM_198491 exon2 c.C79G p.Q27E AGAACTGCCCAAA . 78.0 23.0 60.0 0.0 . 29 . . . none . . PASS Atlas-SNP PIK3R5 23533 hgsc.bcm.edu hg19 17 8794161 8794161 + Missense_Mutation SNP G G A novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . PIK3R5 NM_001142633 exon7 c.C551T p.T184M CCGGGCGTACTCA . 48.0 23.0 35.0 0.0 . 79 . . . none . . PASS Atlas-SNP SMCR8 140775 hgsc.bcm.edu hg19 17 18220533 18220533 + Missense_Mutation SNP C C T novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . SMCR8 NM_144775 exon1 c.C1430T p.T477M TGGGCACGGAGAA . 52.0 14.0 39.0 0.0 . 62 . . . none . . PASS Atlas-SNP KSR1 8844 hgsc.bcm.edu hg19 17 25919618 25919618 + Missense_Mutation SNP A A G novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . KSR1 NM_014238 exon9 c.A854G p.H285R AACCCCATTTTGG . 91.0 34.0 68.0 0.0 . 151 . . . none . . PASS Atlas-SNP NR1D1 9572 hgsc.bcm.edu hg19 17 38249443 38249443 + Silent SNP A A G novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . NR1D1 NM_021724 exon8 c.T1738C p.L580L TCTCCAAGGGCCG . 81.0 57.0 60.0 0.0 . 45 . . . none . . PASS Atlas-SNP AZI1 22994 hgsc.bcm.edu hg19 17 79166382 79166382 + Missense_Mutation SNP T T C novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . AZI1 NM_014984 exon20 c.A2441G p.E814G TCCAGCTCCGCCC . 64.0 18.0 54.0 0.0 . 145 . . . none . . PASS Atlas-SNP TGIF1 7050 hgsc.bcm.edu hg19 18 3457644 3457644 + Silent SNP T T C novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . TGIF1 NM_170695 exon3 c.T912C p.H304H CTGCCATACCACT . 81.0 25.0 85.0 0.0 . 41 . . . none . . PASS Atlas-SNP GADD45B 4616 hgsc.bcm.edu hg19 19 2477521 2477521 + Missense_Mutation SNP G G C novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . GADD45B NM_015675 exon4 c.G405C p.L135F CGGCTTGGTGGAG . 35.0 17.0 20.0 0.0 . 6 . . . none . . PASS Atlas-SNP ZNF283 284349 hgsc.bcm.edu hg19 19 44341266 44341266 + Missense_Mutation SNP A A T novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . ZNF283 NM_181845 exon6 c.A272T p.D91V GCCTGGACCCTGC . 92.0 33.0 82.0 0.0 . 83 . . . none . . PASS Atlas-SNP SYMPK 8189 hgsc.bcm.edu hg19 19 46355636 46355636 + Missense_Mutation SNP A A G novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . SYMPK NM_004819 exon5 c.T233C p.I78T AATGCGATGATCT . 101.0 37.0 112.0 0.0 . 104 . . . none . . PASS Atlas-SNP ZNF649 65251 hgsc.bcm.edu hg19 19 52394350 52394350 + Nonsense_Mutation SNP C C A novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . ZNF649 NM_023074 exon5 c.G1039T p.G347X TGCATCCATAAGG . 79.0 30.0 71.0 0.0 . 72 . . . none . . PASS Atlas-SNP CTCFL 140690 hgsc.bcm.edu hg19 20 56098332 56098332 + Silent SNP G G A novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . CTCFL NM_001269044 exon2 c.C546T p.L182L TTCCTCGAGCTAA . 163.0 67.0 146.0 0.0 . 97 . . . none . . PASS Atlas-SNP THOC2 57187 hgsc.bcm.edu hg19 X 122766884 122766884 + Missense_Mutation SNP T T C novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . THOC2 NM_001081550 exon21 c.A2144G p.Y715C CCAAAATAACCAC . 64.0 49.0 59.0 0.0 . 310 . . . none . . PASS Atlas-SNP SMCR8 140775 hgsc.bcm.edu hg19 17 18220521 18220521 + Frame_Shift_Del DEL A A - novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . SMCR8 NM_144775 exon1 c.1417delG p.E473fs . . 51.0 15.0 49.0 0.0 . 62 . 0.294118 0 none . . PASS Atlas-Indel,Pindel SLC9A4 389015 hgsc.bcm.edu hg19 2 103120119 103120119 + Frame_Shift_Del DEL T T - novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . SLC9A4 NM_001011552 exon3 c.932delA p.Y311fs . . 227.0 68.0 211.0 0.0 . 115 . 0.299559 0 none . . PASS Atlas-Indel,Pindel HNRNPAB 3182 hgsc.bcm.edu hg19 5 177632987 177632988 + Frame_Shift_Ins INS - - A novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . HNRNPAB NM_004499 exon3 c.354_355insA p.F118fs . . 124.0 54.0 124.0 0.0 . 24 . 0.435484 0 none . . PASS Atlas-Indel,Pindel GUCY2C 2984 hgsc.bcm.edu hg19 12 14822676 14822676 + Frame_Shift_Del DEL G G - novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . GUCY2C NM_004963 exon10 c.1263delT p.P421fs . . 62.0 20.0 58.0 0.0 . 126 . 0.322581 0 none . . PASS Atlas-Indel,Pindel VPS52 6293 hgsc.bcm.edu hg19 6 33231610 33231610 + Frame_Shift_Del DEL G G - novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . VPS52 NM_022553 exon16 c.1668delA p.S556fs . . 70.0 22.0 55.0 0.0 . 56 . 0.314286 0 none . . PASS Atlas-Indel,Pindel DIEXF 27042 hgsc.bcm.edu hg19 1 210010373 210010380 + Frame_Shift_Del DEL CTACCCGG CTACCCGG - novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 CTACCCGG CTACCCGG . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . DIEXF NM_014388 exon6 c.878_885del p.293_295del . . 65.0 28.0 77.0 0.0 . 97 . 0.430769 0 none . . PASS Atlas-Indel,Pindel EPS8L1 54869 hgsc.bcm.edu hg19 19 55593489 55593489 + Frame_Shift_Del DEL C C - novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . EPS8L1 NM_133180 exon10 c.930delG p.P310fs . . 109.0 42.0 111.0 0.0 . 122 . 0.385321 0 none . . PASS Atlas-Indel,Pindel LRRC8D 55144 hgsc.bcm.edu hg19 1 90399389 90399389 + Frame_Shift_Del DEL C C - novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . LRRC8D NM_018103 exon3 c.761delT p.I254fs . . 51.0 19.0 47.0 0.0 . 78 . 0.372549 0 none . . PASS Atlas-INDEL SPAG17 200162 hgsc.bcm.edu hg19 1 118509280 118509281 + Frame_Shift_Ins INS - - A novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . SPAG17 NM_206996 exon47 c.6484_6485insT p.I2162fs . . 148.0 58.0 115.0 0.0 . 263 . 0.391892 0 none . . PASS Atlas-Indel,Pindel C1orf173 127254 hgsc.bcm.edu hg19 1 75072484 75072484 + Frame_Shift_Del DEL T T - novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . C1orf173 NM_001002912 exon10 c.1291delG p.V431X . . 424.0 157.0 334.0 0.0 . 380 . 0.370283 0 none . . PASS Atlas-Indel,Pindel LRRC8D 55144 hgsc.bcm.edu hg19 1 90399387 90399390 + Frame_Shift_Del DEL ATCA ATCA - novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 ATCA ATCA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . LRRC8D NM_018103 exon3 c.759_762del p.253_254del . . 55.0 10.0 50.0 0.0 . 78 . 0.182 . none . . PASS Pindel MZT2B 80097 hgsc.bcm.edu hg19 2 130948157 130948157 + Frame_Shift_Del DEL G G - novel TCGA-SX-A7SN-01A-11D-A34Z-10 TCGA-SX-A7SN-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d71c98f8-db62-494f-8677-8997e476ee98 7b35d4fc-dac8-427e-b9c4-1acb0a501501 . MZT2B NM_025029 exon3 c.434delA p.K145fs . . 132.0 36.0 115.0 0.0 . 5 . 0.273 . none . . PASS Pindel