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 dbSNP_AF Algorithm SPTA1 6708 hgsc.bcm.edu hg19 1 158651408 158651408 + Missense_Mutation SNP G G A novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . SPTA1 NM_003126 exon4 c.C440T p.T147I TCCAGGGTCAGCT . 224.0 16.0 281.0 0.0 . 720 . . Atlas-SNP PTPN14 5784 hgsc.bcm.edu hg19 1 214557735 214557735 + Missense_Mutation SNP G G T rs144475962 alternate_allele TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 PTPN14,NS,malignant_melanoma,0,1 PTPN14 NM_005401 exon13 c.C1463A p.P488Q ATCTCCGGTTGGC . 329.0 23.0 392.0 1.0 . 168 . G|0.999;A|0.001 Atlas-SNP C1orf65 164127 hgsc.bcm.edu hg19 1 223568584 223568584 + Silent SNP C C T novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . C1orf65 NM_152610 exon1 c.C1767T p.L589L GAAGCTCCCTCAG . 115.0 9.0 138.0 0.0 . 71 . . Atlas-SNP OBSCN 84033 hgsc.bcm.edu hg19 1 228495849 228495849 + Silent SNP G G T novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . OBSCN NM_001271223 exon58 c.G15375T p.A5125A TGATGCGGAGGTG . 129.0 9.0 168.0 0.0 . 2142 . . Atlas-SNP ZNF638 27332 hgsc.bcm.edu hg19 2 71658550 71658550 + Missense_Mutation SNP T T G rs201989581 alternate_allele TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . ZNF638 NM_014497 exon26 c.T5744G p.V1915G CTGATGTCCCTGA . 292.0 12.0 404.0 0.0 . 179 . T|0.999;C|0.001 Atlas-SNP NCL 4691 hgsc.bcm.edu hg19 2 232325420 232325420 + Missense_Mutation SNP A A T novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . NCL NM_005381 exon4 c.T771A p.D257E TTCATCATCATCA . 322.0 41.0 258.0 0.0 . 80 . . Atlas-SNP NCL 4691 hgsc.bcm.edu hg19 2 232325423 232325423 + Missense_Mutation SNP A A T rs375194579 alternate_allele TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . NCL NM_005381 exon4 c.T768A p.D256E ATCATCATCATCT . 384.0 36.0 473.0 0.0 . 80 . . Atlas-SNP USP40 55230 hgsc.bcm.edu hg19 2 234394446 234394446 + Silent SNP G G A novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . USP40 NM_018218 exon28 c.C3408T p.P1136P CTTTTCGGGAAAG . 335.0 21.0 438.0 0.0 . 174 . . Atlas-SNP IFT57 55081 hgsc.bcm.edu hg19 3 107937444 107937444 + Silent SNP T T C novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . IFT57 NM_018010 exon3 c.A432G p.V144V ATAGCATACATGT . 307.0 13.0 393.0 0.0 . 44 . . Atlas-SNP ARHGAP10 79658 hgsc.bcm.edu hg19 4 148886196 148886196 + Missense_Mutation SNP G G A novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . ARHGAP10 NM_024605 exon17 c.G1472A p.R491H AATCTCGTGTTAA . 466.0 23.0 561.0 0.0 . 92 . . Atlas-SNP SGTB 54557 hgsc.bcm.edu hg19 5 64976616 64976616 + Missense_Mutation SNP G G A novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . SGTB NM_019072 exon7 c.C485T p.A162V GTGAGGGCCAGCC . 136.0 9.0 182.0 0.0 . 22 . . Atlas-SNP C6orf106 64771 hgsc.bcm.edu hg19 6 34574641 34574641 + Silent SNP A A C novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . C6orf106 NM_024294 exon4 c.T552G p.L184L TCCTAAAAGTCCA . 67.0 8.0 91.0 0.0 . 29 . . Atlas-SNP GJB7 375519 hgsc.bcm.edu hg19 6 87994213 87994213 + Missense_Mutation SNP C C T novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . GJB7 NM_198568 exon3 c.G418A p.V140I ATAAAACAAGGAA . 79.0 16.0 99.0 0.0 . 28 . . Atlas-SNP GUSB 2990 hgsc.bcm.edu hg19 7 65440043 65440043 + Nonsense_Mutation SNP G G A novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . GUSB NM_000181 exon6 c.C928T p.Q310X ACGTCTGTGCAGT . 68.0 9.0 80.0 0.0 . 52 . . Atlas-SNP LRRCC1 85444 hgsc.bcm.edu hg19 8 86057622 86057622 + Splice_Site SNP A A T novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 LRRCC1_ENST00000414626,NS,carcinoma,0,2 LRRCC1 NM_033402 exon19 c.2977-2A>T . CGATTTAGGTCCA . 438.0 27.0 463.0 2.0 . 212 . . Atlas-SNP CTHRC1 115908 hgsc.bcm.edu hg19 8 104388131 104388131 + Missense_Mutation SNP T T A novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . CTHRC1 NM_138455 exon2 c.T316A p.Y106N CCCAACTACAAGC . 143.0 8.0 147.0 0.0 . 29 . . Atlas-SNP ABRA 137735 hgsc.bcm.edu hg19 8 107782232 107782232 + Missense_Mutation SNP G G C novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 ABRA,NS,carcinoma,0,1 ABRA NM_139166 exon1 c.C187G p.P63A GTTTAGGAGCTTG . 354.0 32.0 573.0 0.0 . 57 . . Atlas-SNP OLFML2A 169611 hgsc.bcm.edu hg19 9 127561615 127561615 + Missense_Mutation SNP C C A novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . OLFML2A NM_182487 exon4 c.C514A p.R172S AGCGTGCGCCACC . 125.0 10.0 159.0 0.0 . 61 . . Atlas-SNP HIF1A 3091 hgsc.bcm.edu hg19 14 62207716 62207716 + Missense_Mutation SNP A A T novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . HIF1A NM_001243084 exon12 c.A1975T p.I659F GAAGACATTAAAA . 159.0 9.0 235.0 0.0 . 120 . . Atlas-SNP AHNAK2 113146 hgsc.bcm.edu hg19 14 105419292 105419292 + Missense_Mutation SNP C C A novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . AHNAK2 NM_138420 exon7 c.G2496T p.K832N TTTGAACTTGCTG . 228.0 13.0 323.0 0.0 . 719 . . Atlas-SNP URI1 8725 hgsc.bcm.edu hg19 19 30476164 30476164 + Missense_Mutation SNP G G A novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . . NM_003796 exon3 c.G187A p.E63K CTTCGAGAAAGAC . 263.0 15.0 359.0 0.0 . . . . Atlas-SNP SON 6651 hgsc.bcm.edu hg19 21 34925206 34925206 + Silent SNP T T A novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . SON NM_032195 exon3 c.T3669A p.P1223P GGAGCCTTCAGCA . 237.0 14.0 282.0 0.0 . 343 . . Atlas-SNP HMGB3 3149 hgsc.bcm.edu hg19 X 150155724 150155724 + Missense_Mutation SNP A A T novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . HMGB3 NM_005342 exon4 c.A414T p.E138D CAGTGAAAAGCAG . 158.0 11.0 219.0 0.0 . 27 . . Atlas-SNP FILIP1 27145 hgsc.bcm.edu hg19 6 76018525 76018526 + Frame_Shift_Ins INS - - C novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . FILIP1 NM_015687 exon6 c.3524_3525insG p.A1175fs . . 214.0 17.0 455.0 0.0 . 173 . . Atlas-INDEL ARFGAP2 84364 hgsc.bcm.edu hg19 11 47187860 47187861 + Frame_Shift_Ins INS - - C novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . ARFGAP2 NM_032389 exon15 c.1504_1505insG p.K502fs . . 121.0 16.0 210.0 0.0 . 43 . . Atlas-INDEL TNKS1BP1 85456 hgsc.bcm.edu hg19 11 57077359 57077360 + Frame_Shift_Ins INS - - C novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . TNKS1BP1 NM_033396 exon6 c.2826_2827insG p.S942fs . . 118.0 10.0 158.0 0.0 . 148 . . Atlas-INDEL SMARCC1 6599 hgsc.bcm.edu hg19 3 47629720 47629721 + Frame_Shift_Ins INS - - G rs35867350 TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . SMARCC1 NM_003074 exon28 c.3297_3298insC p.P1099fs . . 116.0 11.0 151.0 0.0 . 85 . . Atlas-INDEL ZNF233 353355 hgsc.bcm.edu hg19 19 44778797 44778797 + Frame_Shift_Del DEL T T - novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 .,8 ZNF233 NM_001207005 exon5 c.1983delG p.S661fs . . 88.0 81.0 109.0 0.0 . 73 . . Atlas-INDEL COL17A1 1308 hgsc.bcm.edu hg19 10 105837253 105837254 + Frame_Shift_Ins INS - - G novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . COL17A1 NM_000494 exon4 c.129_130insC p.T43fs . . 101.0 10.0 144.0 0.0 . 149 . . Atlas-INDEL TENM2 57451 hgsc.bcm.edu hg19 5 167645298 167645299 + Frame_Shift_Ins INS - - T novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . . NM_001122679 exon23 c.4375_4376insT p.L1459fs . . 115.0 12.0 174.0 0.0 . . . . Atlas-INDEL SUMF2 25870 hgsc.bcm.edu hg19 7 56144554 56144555 + Frame_Shift_Ins INS - - C novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . SUMF2 NM_015411 exon6 c.620_621insC p.F207fs . . 140.0 10.0 207.0 0.0 . 56 . . Atlas-INDEL IFT88 8100 hgsc.bcm.edu hg19 13 21219024 21219025 + Frame_Shift_Ins INS - - T novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . IFT88 NM_175605 exon22 c.1903_1904insT p.L635fs . . 279.0 17.0 300.0 0.0 . 83 . . Atlas-INDEL KRTAP19-8 728299 hgsc.bcm.edu hg19 21 32410712 32410713 + Frame_Shift_Ins INS - - C novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . KRTAP19-8 NM_001099219 exon1 c.51_52insG p.G17fs . . 134.0 10.0 216.0 0.0 . 9 . . Atlas-INDEL MSH5 4439 hgsc.bcm.edu hg19 6 31729664 31729665 + Frame_Shift_Ins INS - - C novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . MSH5 NM_172165 exon23 c.2254_2255insC p.A752fs . . 169.0 11.0 224.0 0.0 . 108 . . Atlas-INDEL ARAP1 116985 hgsc.bcm.edu hg19 11 72407643 72407644 + Frame_Shift_Ins INS - - C novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . ARAP1 NM_001040118 exon23 c.3223_3224insG p.P1075fs . . 54.0 10.0 109.0 0.0 . 168 . . Atlas-INDEL PKP1 5317 hgsc.bcm.edu hg19 1 201293599 201293600 + Frame_Shift_Ins INS - - C novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 .,2 PKP1 NM_000299 exon11 c.1787_1788insC p.G596fs . . 78.0 10.0 106.0 0.0 . 127 . . Atlas-INDEL TLN1 7094 hgsc.bcm.edu hg19 9 35725253 35725254 + Frame_Shift_Ins INS - - C novel TCGA-BC-A110-01A-11D-A12Z-10 TCGA-BC-A110-11A-11D-A12Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7df1cd46-d00e-474c-9815-b41edb5ccf20 10045d1f-6bbd-4855-878e-90705d76e6f8 . TLN1 NM_006289 exon3 c.196_197insG p.K66fs . . 136.0 12.0 175.0 0.0 . 185 . . Atlas-INDEL