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 ARHGEF19 128272 hgsc.bcm.edu hg19 1 16532674 16532674 + Splice_Site SNP C C T novel TCGA-4A-A93Y-01A-11D-A36X-10 TCGA-4A-A93Y-10A-01D-A370-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90 8502bb1a-6a04-42ad-88f1-4559e24b1286 . ARHGEF19 NM_153213 exon8 c.1298+1G>A . TCTTCACCTCTCG . 108.0 7.0 111.0 0.0 . 49 . . . none . . PASS Atlas-SNP OLFML2B 25903 hgsc.bcm.edu hg19 1 161953624 161953624 + Nonsense_Mutation SNP G G T rs150437510 bycluster;byfrequency;alternate_allele TCGA-4A-A93Y-01A-11D-A36X-10 TCGA-4A-A93Y-10A-01D-A370-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90 8502bb1a-6a04-42ad-88f1-4559e24b1286 . OLFML2B NM_015441 exon8 c.C2094A p.Y698X GAAAGCGTAGGAG . 197.0 13.0 200.0 0.0 . 114 . . . alt G|1.000;A|0.000 . PASS Atlas-SNP MPC2 25874 hgsc.bcm.edu hg19 1 167893755 167893755 + Missense_Mutation SNP A A G novel TCGA-4A-A93Y-01A-11D-A36X-10 TCGA-4A-A93Y-10A-01D-A370-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90 8502bb1a-6a04-42ad-88f1-4559e24b1286 . . NM_001143674 exon3 c.T130C p.W44R GAGCCCAGAAGAA . 550.0 24.0 552.0 0.0 . . . . . none . . PASS Atlas-SNP ZNF142 7701 hgsc.bcm.edu hg19 2 219508733 219508733 + Missense_Mutation SNP A A T novel TCGA-4A-A93Y-01A-11D-A36X-10 TCGA-4A-A93Y-10A-01D-A370-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90 8502bb1a-6a04-42ad-88f1-4559e24b1286 . ZNF142 NM_001105537 exon8 c.T2506A p.F836I AGCGGAAGGCTCG . 126.0 10.0 159.0 0.0 . 190 . . . none . . PASS Atlas-SNP C3orf80 401097 hgsc.bcm.edu hg19 3 159943902 159943902 + Silent SNP T T C novel TCGA-4A-A93Y-01A-11D-A36X-10 TCGA-4A-A93Y-10A-01D-A370-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90 8502bb1a-6a04-42ad-88f1-4559e24b1286 . C3orf80 NM_001168214 exon1 c.T480C p.S160S GGACAGTGGCGGC . 6.0 5.0 0.0 0.0 . 1 . . . none . . PASS Atlas-SNP CXXC4 80319 hgsc.bcm.edu hg19 4 105412357 105412357 + Silent SNP T T C novel TCGA-4A-A93Y-01A-11D-A36X-10 TCGA-4A-A93Y-10A-01D-A370-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90 8502bb1a-6a04-42ad-88f1-4559e24b1286 . CXXC4 NM_025212 exon2 c.A603G p.L201L AGGGGATAAGGTG . 90.0 7.0 78.0 0.0 . 20 . . . none . . PASS Atlas-SNP RUNX2 860 hgsc.bcm.edu hg19 6 45390445 45390445 + Silent SNP A A G novel TCGA-4A-A93Y-01A-11D-A36X-10 TCGA-4A-A93Y-10A-01D-A370-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90 8502bb1a-6a04-42ad-88f1-4559e24b1286 RUNX2_ENST00000352853,lower_third,carcinoma,0,2 RUNX2 NM_001024630 exon3 c.A174G p.Q58Q GCAGCAACAGCAG . 65.0 3.0 79.0 0.0 . 128 . . . none . . PASS Atlas-SNP GPR126 57211 hgsc.bcm.edu hg19 6 142714109 142714109 + Missense_Mutation SNP A A T novel TCGA-4A-A93Y-01A-11D-A36X-10 TCGA-4A-A93Y-10A-01D-A370-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90 8502bb1a-6a04-42ad-88f1-4559e24b1286 . GPR126 NM_198569 exon8 c.A1333T p.N445Y AATTGGAACTACA . 139.0 8.0 149.0 0.0 . 192 . . . none . . PASS Atlas-SNP SP4 6671 hgsc.bcm.edu hg19 7 21468306 21468306 + Missense_Mutation SNP G G A novel TCGA-4A-A93Y-01A-11D-A36X-10 TCGA-4A-A93Y-10A-01D-A370-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90 8502bb1a-6a04-42ad-88f1-4559e24b1286 SP4,colon,carcinoma,0,1 SP4 NM_003112 exon2 c.G19A p.E7K AAGAAGGAGGAGG . 143.0 6.0 105.0 1.0 . 91 . . . none . . PASS Atlas-SNP PLXNA4 91584 hgsc.bcm.edu hg19 7 131859623 131859623 + Missense_Mutation SNP C C T novel TCGA-4A-A93Y-01A-11D-A36X-10 TCGA-4A-A93Y-10A-01D-A370-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90 8502bb1a-6a04-42ad-88f1-4559e24b1286 . PLXNA4 NM_020911 exon21 c.G3931A p.G1311R GAATCCCGGCTCC . 100.0 7.0 94.0 0.0 . 873 . . . none . . PASS Atlas-SNP CNTLN 54875 hgsc.bcm.edu hg19 9 17330790 17330790 + Missense_Mutation SNP C C A novel TCGA-4A-A93Y-01A-11D-A36X-10 TCGA-4A-A93Y-10A-01D-A370-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90 8502bb1a-6a04-42ad-88f1-4559e24b1286 . CNTLN NM_017738 exon9 c.C1502A p.A501D CAAGTGCTGAAGG . 367.0 16.0 384.0 0.0 . 128 . . . none . . PASS Atlas-SNP OR6Q1 219952 hgsc.bcm.edu hg19 11 57798465 57798465 + Missense_Mutation SNP T T A novel TCGA-4A-A93Y-01A-11D-A36X-10 TCGA-4A-A93Y-10A-01D-A370-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90 8502bb1a-6a04-42ad-88f1-4559e24b1286 . OR6Q1 NM_001005186 exon1 c.T41A p.F14Y CTGAATTTGTCAT . 145.0 14.0 127.0 0.0 . 58 . . . none . . PASS Atlas-SNP FIGNL2 401720 hgsc.bcm.edu hg19 12 52215801 52215801 + Missense_Mutation SNP G G T novel TCGA-4A-A93Y-01A-11D-A36X-10 TCGA-4A-A93Y-10A-01D-A370-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90 8502bb1a-6a04-42ad-88f1-4559e24b1286 . . NM_001013690 exon2 c.C397A p.P133T AAACTGGGGAGCC . 140.0 12.0 164.0 0.0 . . . . . none . . PASS Atlas-SNP LRP1 4035 hgsc.bcm.edu hg19 12 57589521 57589521 + Missense_Mutation SNP G G T novel TCGA-4A-A93Y-01A-11D-A36X-10 TCGA-4A-A93Y-10A-01D-A370-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90 8502bb1a-6a04-42ad-88f1-4559e24b1286 . LRP1 NM_002332 exon53 c.G8518T p.D2840Y GACCACGACCGTG . 120.0 10.0 119.0 0.0 . 428 . . . none . . PASS Atlas-SNP LTK 4058 hgsc.bcm.edu hg19 15 41797955 41797955 + Silent SNP C C T rs375203744 TCGA-4A-A93Y-01A-11D-A36X-10 TCGA-4A-A93Y-10A-01D-A370-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90 8502bb1a-6a04-42ad-88f1-4559e24b1286 . LTK NM_002344 exon13 c.G1653A p.S551S CTGAGGCGAGCAG . 264.0 12.0 250.0 0.0 . 117 . . . weak . . PASS Atlas-SNP CREBBP 1387 hgsc.bcm.edu hg19 16 3786685 3786685 + Missense_Mutation SNP T T C novel TCGA-4A-A93Y-01A-11D-A36X-10 TCGA-4A-A93Y-10A-01D-A370-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90 8502bb1a-6a04-42ad-88f1-4559e24b1286 . CREBBP NM_004380 exon27 c.A4526G p.K1509R AACGCCTTGTCCA . 111.0 5.0 156.0 0.0 . 546 . . . none . . PASS Atlas-SNP CACNG3 10368 hgsc.bcm.edu hg19 16 24358125 24358125 + Silent SNP C C T novel TCGA-4A-A93Y-01A-11D-A36X-10 TCGA-4A-A93Y-10A-01D-A370-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90 8502bb1a-6a04-42ad-88f1-4559e24b1286 . CACNG3 NM_006539 exon2 c.C282T p.A94A CACAGCCGAATAT . 96.0 7.0 80.0 0.0 . 112 . . . none . . PASS Atlas-SNP DHX38 9785 hgsc.bcm.edu hg19 16 72133644 72133644 + Missense_Mutation SNP A A T novel TCGA-4A-A93Y-01A-11D-A36X-10 TCGA-4A-A93Y-10A-01D-A370-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90 8502bb1a-6a04-42ad-88f1-4559e24b1286 . DHX38 NM_014003 exon8 c.A974T p.D325V ATCGGGATTGGTA . 113.0 9.0 118.0 0.0 . 91 . . . none . . PASS Atlas-SNP NCOR1 9611 hgsc.bcm.edu hg19 17 15965099 15965099 + Missense_Mutation SNP G G T novel TCGA-4A-A93Y-01A-11D-A36X-10 TCGA-4A-A93Y-10A-01D-A370-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90 8502bb1a-6a04-42ad-88f1-4559e24b1286 . NCOR1 NM_001190440 exon36 c.C5545A p.Q1849K CCATCTGGGGTGC . 113.0 5.0 144.0 0.0 . 240 . . . none . . PASS Atlas-SNP SUZ12 23512 hgsc.bcm.edu hg19 17 30315477 30315477 + Nonsense_Mutation SNP G G T novel TCGA-4A-A93Y-01A-11D-A36X-10 TCGA-4A-A93Y-10A-01D-A370-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90 8502bb1a-6a04-42ad-88f1-4559e24b1286 . SUZ12 NM_015355 exon10 c.G1162T p.E388X CATCAGGAAAACA . 267.0 14.0 263.0 0.0 . 61 . . . none . . PASS Atlas-SNP SYCP2 10388 hgsc.bcm.edu hg19 20 58445040 58445040 + Splice_Site SNP T T G novel TCGA-4A-A93Y-01A-11D-A36X-10 TCGA-4A-A93Y-10A-01D-A370-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90 8502bb1a-6a04-42ad-88f1-4559e24b1286 . SYCP2 NM_014258 exon36 c.3556-2A>C . CTGGGCTATGAAT . 71.0 10.0 41.0 0.0 . 204 . . . none . . PASS Atlas-SNP MXRA5 25878 hgsc.bcm.edu hg19 X 3235245 3235245 + Missense_Mutation SNP C C A novel TCGA-4A-A93Y-01A-11D-A36X-10 TCGA-4A-A93Y-10A-01D-A370-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90 8502bb1a-6a04-42ad-88f1-4559e24b1286 . MXRA5 NM_015419 exon6 c.G6477T p.R2159S TCCGTACCTGACG . 218.0 10.0 201.0 0.0 . 815 . . . none . . PASS Atlas-SNP MXRA5 25878 hgsc.bcm.edu hg19 X 3235246 3235246 + Missense_Mutation SNP C C A novel TCGA-4A-A93Y-01A-11D-A36X-10 TCGA-4A-A93Y-10A-01D-A370-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90 8502bb1a-6a04-42ad-88f1-4559e24b1286 . MXRA5 NM_015419 exon6 c.G6476T p.R2159M CCGTACCTGACGT . 219.0 10.0 203.0 0.0 . 815 . . . none . . PASS Atlas-SNP COX1 5742 hgsc.bcm.edu hg19 MT 7020 7020 + Missense_Mutation SNP G G A novel TCGA-4A-A93Y-01A-11D-A36X-10 TCGA-4A-A93Y-10A-01D-A370-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90 8502bb1a-6a04-42ad-88f1-4559e24b1286 . . ENST00000361624 exon1 c.G1117A p.V373I TACTACGTTGTAG . 129.0 11.0 15.0 0.0 . . . . . none . . PASS Atlas-SNP HEG1 57493 hgsc.bcm.edu hg19 3 124732430 124732431 + In_Frame_Ins INS - - GGAAGAGGAGGAGGAGGA novel TCGA-4A-A93Y-01A-11D-A36X-10 TCGA-4A-A93Y-10A-01D-A370-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90 8502bb1a-6a04-42ad-88f1-4559e24b1286 . HEG1 NM_020733 exon6 c.1993_1994insTCCTCCTCCTCCTCTTCC p.S665delinsSSSSSSS . . 110.0 11.0 95.0 0.0 . 109 . 0.1 0 none . . PASS Atlas-INDEL SUSD1 64420 hgsc.bcm.edu hg19 9 114864480 114864480 + Frame_Shift_Del DEL T T - novel TCGA-4A-A93Y-01A-11D-A36X-10 TCGA-4A-A93Y-10A-01D-A370-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90 8502bb1a-6a04-42ad-88f1-4559e24b1286 . SUSD1 NM_022486 exon9 c.1258delG p.V420fs . . 276.0 18.0 252.0 0.0 . 51 . 0.0652174 0 none . . PASS Atlas-Indel,Pindel ABCC6 368 hgsc.bcm.edu hg19 16 16302617 16302618 + Frame_Shift_Ins INS - - T novel TCGA-4A-A93Y-01A-11D-A36X-10 TCGA-4A-A93Y-10A-01D-A370-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq ecd232a0-9ac6-4eda-8f3e-8ab73e39ce90 8502bb1a-6a04-42ad-88f1-4559e24b1286 . ABCC6 NM_001171 exon7 c.762_763insA p.K254fs . . 465.0 22.0 459.0 0.0 . 110 . 0.047 . none . . PASS Pindel