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 VWA5B1 127731 hgsc.bcm.edu hg19 1 20657389 20657389 + Missense_Mutation SNP C C A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . VWA5B1 NM_001039500 exon11 c.C1485A p.N495K ACCCAACGTCTGC . 145.0 81.0 204.0 0.0 . 44 . . Atlas-SNP DNAJC6 9829 hgsc.bcm.edu hg19 1 65775451 65775451 + Missense_Mutation SNP G G A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . DNAJC6 NM_001256864 exon1 c.G23A p.R8Q GCTACCGGAAAAA . 120.0 29.0 146.0 0.0 . 104 . . Atlas-SNP SLC44A5 204962 hgsc.bcm.edu hg19 1 75805298 75805298 + Missense_Mutation SNP C C A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . SLC44A5 NM_152697 exon4 c.G70T p.D24Y CTGGGTCATATGT . 65.0 14.0 74.0 0.0 . 231 . . Atlas-SNP KCNC4 3749 hgsc.bcm.edu hg19 1 110775555 110775555 + Silent SNP G G A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 KCNC4_ENST00000438661,NS,carcinoma,0,1 KCNC4 NM_001039574 exon4 c.G1842A p.S614S CCTCTCGTCCAAC . 37.0 25.0 69.0 0.0 . 113 . . Atlas-SNP PLEKHO1 51177 hgsc.bcm.edu hg19 1 150131276 150131276 + Missense_Mutation SNP C C T novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . PLEKHO1 NM_016274 exon6 c.C788T p.P263L TGACGCCCACAGA . 303.0 15.0 117.0 0.0 . 37 . . Atlas-SNP PLEKHO1 51177 hgsc.bcm.edu hg19 1 150131673 150131673 + Silent SNP C C G novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 PLEKHO1,bladder,carcinoma,0,1 PLEKHO1 NM_016274 exon6 c.C1185G p.L395L CCACCTCAGACAG . 390.0 16.0 165.0 0.0 . 37 . . Atlas-SNP DHX9 1660 hgsc.bcm.edu hg19 1 182823304 182823304 + Missense_Mutation SNP A A G novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . DHX9 NM_001357 exon6 c.A617G p.D206G GTCCTGATCACAA . 166.0 100.0 223.0 0.0 . 114 . . Atlas-SNP TRIM54 57159 hgsc.bcm.edu hg19 2 27528584 27528584 + Missense_Mutation SNP G G C novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . TRIM54 NM_032546 exon6 c.G868C p.G290R GTCCGCGGCCTCA . 79.0 33.0 100.0 0.0 . 35 . . Atlas-SNP LOC728819 0 hgsc.bcm.edu hg19 2 43903342 43903342 + Silent SNP G G A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . . NM_001101330 exon1 c.C120T p.H40H GTGCTCGTGGTCT . 377.0 173.0 448.0 0.0 . . . . Atlas-SNP TCF7L1 83439 hgsc.bcm.edu hg19 2 85361140 85361140 + Missense_Mutation SNP C C A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . TCF7L1 NM_031283 exon2 c.C251A p.A84E CGCAGGCGGAGAG . 41.0 24.0 80.0 0.0 . 44 . . Atlas-SNP RANBP2 5903 hgsc.bcm.edu hg19 2 109381074 109381074 + Missense_Mutation SNP G G A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . RANBP2 NM_006267 exon20 c.G4079A p.S1360N GTAACAGCTGCTC . 112.0 53.0 157.0 0.0 . 488 . . Atlas-SNP KCNJ3 3760 hgsc.bcm.edu hg19 2 155555841 155555841 + Missense_Mutation SNP C C A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . KCNJ3 NM_001260509 exon1 c.C554A p.S185Y AGATGTCCCAGCC . 79.0 17.0 87.0 0.0 . 126 . . Atlas-SNP XIRP2 129446 hgsc.bcm.edu hg19 2 168100239 168100239 + Missense_Mutation SNP G G T novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . XIRP2 NM_152381 exon9 c.G2337T p.L779F GCCGTTGGACACA . 230.0 114.0 305.0 0.0 . 914 . . Atlas-SNP OSBPL6 114880 hgsc.bcm.edu hg19 2 179170928 179170928 + Missense_Mutation SNP A A G novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . OSBPL6 NM_001201482 exon3 c.A17G p.K6R ATGAGAAGGGCAT . 83.0 46.0 110.0 0.0 . 178 . . Atlas-SNP HIBCH 26275 hgsc.bcm.edu hg19 2 191155206 191155206 + Missense_Mutation SNP A A C novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . HIBCH NM_014362 exon5 c.T310G p.S104A CTTCCGAGATCAC . 135.0 58.0 136.0 0.0 . 28 . . Atlas-SNP DNAH7 56171 hgsc.bcm.edu hg19 2 196825086 196825086 + Missense_Mutation SNP A A G novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . DNAH7 NM_018897 exon18 c.T2789C p.L930S GATGCCAAAATAA . 98.0 44.0 108.0 0.0 . 512 . . Atlas-SNP SGOL2 151246 hgsc.bcm.edu hg19 2 201400832 201400832 + Missense_Mutation SNP G G C novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 SGOL2,bladder,carcinoma,0,1 SGOL2 NM_001160046 exon4 c.G354C p.L118F TAACTTGATAACT . 97.0 40.0 101.0 0.0 . 126 . . Atlas-SNP ABI2 10152 hgsc.bcm.edu hg19 2 204193320 204193320 + Missense_Mutation SNP G G T novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . ABI2 NM_005759 exon1 c.G83T p.R28L TGGAACGGGTGGC . 80.0 34.0 104.0 0.0 . 44 . . Atlas-SNP DYTN 391475 hgsc.bcm.edu hg19 2 207530732 207530732 + Missense_Mutation SNP G G T novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . DYTN NM_001093730 exon10 c.C1002A p.N334K GTATTGGTTTAAC . 283.0 131.0 364.0 1.0 . 168 . . Atlas-SNP NBEAL2 23218 hgsc.bcm.edu hg19 3 47030821 47030821 + Silent SNP C C G novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . NBEAL2 NM_015175 exon5 c.C423G p.L141L GCTTCTCTGCGAG . 74.0 29.0 91.0 0.0 . 267 . . Atlas-SNP ROBO2 6092 hgsc.bcm.edu hg19 3 77629195 77629195 + Missense_Mutation SNP A A C novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . ROBO2 NM_002942 exon16 c.A2426C p.Q809P GTATTCAATACCG . 98.0 86.0 206.0 0.0 . 527 . . Atlas-SNP KIAA1407 57577 hgsc.bcm.edu hg19 3 113737618 113737618 + Missense_Mutation SNP A A T novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . KIAA1407 NM_020817 exon8 c.T1070A p.L357Q ACCTTCAGCTGAA . 74.0 16.0 86.0 0.0 . 80 . . Atlas-SNP HGD 3081 hgsc.bcm.edu hg19 3 120365198 120365198 + Missense_Mutation SNP T T A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . HGD NM_000187 exon9 c.A565T p.S189C CTATGCTGAACCG . 41.0 20.0 45.0 0.0 . 65 . . Atlas-SNP MYLK 4638 hgsc.bcm.edu hg19 3 123411616 123411616 + Silent SNP G G A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . MYLK NM_053025 exon19 c.C3531T p.G1177G CGCCTGGCCAGCG . 48.0 24.0 81.0 0.0 . 224 . . Atlas-SNP SHOX2 6474 hgsc.bcm.edu hg19 3 157820591 157820591 + Missense_Mutation SNP C C T novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . SHOX2 NM_003030 exon3 c.G503A p.R168Q TTGGTCCGACTTC . 202.0 95.0 264.0 1.0 . 84 . . Atlas-SNP TMEM175 84286 hgsc.bcm.edu hg19 4 944240 944240 + Missense_Mutation SNP C C A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . TMEM175 NM_032326 exon4 c.C224A p.A75E TTCTGGCAACACG . 111.0 44.0 182.0 0.0 . 44 . . Atlas-SNP TBC1D14 57533 hgsc.bcm.edu hg19 4 7026792 7026792 + Missense_Mutation SNP T T C novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 TBC1D14_ENST00000409757,colon,carcinoma,0,2 TBC1D14 NM_001113361 exon13 c.T1819C p.F607L GACGTGTTCTGTC . 203.0 47.0 276.0 1.0 . 110 . . Atlas-SNP TRMT44 152992 hgsc.bcm.edu hg19 4 8469838 8469838 + Silent SNP C C T novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . TRMT44 NM_152544 exon9 c.C1692T p.V564V CAGGGTCGGGTGT . 123.0 5.0 155.0 0.0 . 7 . . Atlas-SNP PCDH7 5099 hgsc.bcm.edu hg19 4 30724910 30724910 + Missense_Mutation SNP C C A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . PCDH7 NM_032457 exon1 c.C1866A p.S622R GGGCAGCACTACG . 89.0 36.0 68.0 0.0 . 215 . . Atlas-SNP PCDH7 5099 hgsc.bcm.edu hg19 4 30725405 30725405 + Missense_Mutation SNP T T A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . PCDH7 NM_032457 exon1 c.T2361A p.N787K AGGAAATCCCTTC . 89.0 38.0 104.0 0.0 . 215 . . Atlas-SNP LPHN3 23284 hgsc.bcm.edu hg19 4 62936605 62936605 + Silent SNP T T C novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . LPHN3 NM_015236 exon23 c.T4389C p.A1463A ACCGGCTCATTTG . 86.0 56.0 69.0 0.0 . 800 . . Atlas-SNP NPY5R 4889 hgsc.bcm.edu hg19 4 164272591 164272591 + Missense_Mutation SNP T T A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . NPY5R NM_006174 exon4 c.T1166A p.V389E TCCATGTGGTAAC . 154.0 86.0 207.0 0.0 . 101 . . Atlas-SNP DDX60 55601 hgsc.bcm.edu hg19 4 169201507 169201507 + Missense_Mutation SNP C C G novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . DDX60 NM_017631 exon14 c.G1957C p.E653Q AATGTTCTTTCCA . 247.0 144.0 307.0 0.0 . 304 . . Atlas-SNP DDX60L 91351 hgsc.bcm.edu hg19 4 169382958 169382958 + Nonsense_Mutation SNP C C T novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . DDX60L NM_001012967 exon5 c.G498A p.W166X CATTCCCCAGGAA . 89.0 30.0 114.0 0.0 . 116 . . Atlas-SNP IRX1 79192 hgsc.bcm.edu hg19 5 3599577 3599577 + Missense_Mutation SNP C C A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . IRX1 NM_024337 exon2 c.C515A p.T172K CCCTCACGCAGGT . 227.0 116.0 236.0 0.0 . 106 . . Atlas-SNP CTNND2 1501 hgsc.bcm.edu hg19 5 10992757 10992757 + Silent SNP C C A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . CTNND2 NM_001332 exon19 c.G3117T p.S1039S TGAAGACGAGGCT . 123.0 60.0 159.0 0.0 . 289 . . Atlas-SNP FSTL4 23105 hgsc.bcm.edu hg19 5 132534838 132534838 + Missense_Mutation SNP C C G novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . FSTL4 NM_015082 exon16 c.G2478C p.E826D TGACACCTCACAC . 66.0 25.0 86.0 0.0 . 74 . . Atlas-SNP PCDHA6 56142 hgsc.bcm.edu hg19 5 140209550 140209550 + Missense_Mutation SNP G G A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . PCDHA6 NM_018909 exon1 c.G1874A p.G625E GCGTGGGGCTGTA . 118.0 49.0 131.0 0.0 . 442 . . Atlas-SNP PCDHAC2 56134 hgsc.bcm.edu hg19 5 140347607 140347607 + Missense_Mutation SNP A A G novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . PCDHAC2 NM_031883 exon1 c.A1256G p.Y419C ACTCCTATACACT . 92.0 49.0 61.0 0.0 . 142 . . Atlas-SNP PCDHB7 56129 hgsc.bcm.edu hg19 5 140554546 140554546 + Silent SNP G G A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . PCDHB7 NM_018940 exon1 c.G2130A p.R710R GGTGCGGCTGTGC . 177.0 28.0 198.0 0.0 . 231 . . Atlas-SNP GPR151 134391 hgsc.bcm.edu hg19 5 145895523 145895523 + Missense_Mutation SNP C C T rs181265546 bycluster;by1000genomes;alternate_allele TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . GPR151 NM_194251 exon1 c.G154A p.V52M TTCCCACGAAGCC . 105.0 17.0 134.0 0.0 . 35 . C|1.000;G|0.000 Atlas-SNP CLK4 57396 hgsc.bcm.edu hg19 5 178040784 178040784 + Silent SNP A A T novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . CLK4 NM_020666 exon6 c.T603A p.A201A TGAACGAGCTGCT . 173.0 65.0 231.0 0.0 . 103 . . Atlas-SNP HIST1H3F 8968 hgsc.bcm.edu hg19 6 26250628 26250628 + Missense_Mutation SNP T T C novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . HIST1H3F NM_021018 exon1 c.A206G p.Q69R AGACGCTGGAATG . 194.0 104.0 191.0 1.0 . 16 . . Atlas-SNP HSPA1L 3305 hgsc.bcm.edu hg19 6 31777908 31777908 + Silent SNP T T C novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . HSPA1L NM_005527 exon2 c.A1842G p.Q614Q TCCTCCTTGGTAG . 413.0 120.0 217.0 0.0 . 185 . . Atlas-SNP CPNE5 57699 hgsc.bcm.edu hg19 6 36712088 36712088 + Silent SNP G G T novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . CPNE5 NM_020939 exon19 c.C1446A p.P482P GGACATGGGGAGC . 80.0 40.0 119.0 0.0 . 56 . . Atlas-SNP DST 667 hgsc.bcm.edu hg19 6 56480865 56480865 + Missense_Mutation SNP C C T rs200851382 TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . DST NM_001723 exon24 c.G7400A p.R2467H TTTCTACGGGAGG . 122.0 30.0 112.0 0.0 . 1427 . C|0.999;T|0.001 Atlas-SNP RIMS1 22999 hgsc.bcm.edu hg19 6 72968729 72968729 + Missense_Mutation SNP C C A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . RIMS1 NM_014989 exon18 c.C2968A p.P990T CGTTCTCCAACCA . 104.0 41.0 98.0 0.0 . 278 . . Atlas-SNP SYNE1 23345 hgsc.bcm.edu hg19 6 152583243 152583243 + Missense_Mutation SNP C C A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . SYNE1 NM_182961 exon101 c.G18896T p.W6299L CTTTCCCATTTCA . 212.0 49.0 238.0 0.0 . 3227 . . Atlas-SNP HGF 3082 hgsc.bcm.edu hg19 7 81339555 81339555 + Silent SNP G G T rs375872396 alternate_allele TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . HGF NM_000601 exon13 c.C1449A p.P483P TATTACGGGATCT . 126.0 58.0 197.0 0.0 . 171 . . Atlas-SNP HGF 3082 hgsc.bcm.edu hg19 7 81339556 81339556 + Missense_Mutation SNP G G T novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . HGF NM_000601 exon13 c.C1448A p.P483H ATTACGGGATCTG . 124.0 59.0 194.0 0.0 . 171 . . Atlas-SNP PLXNA4 91584 hgsc.bcm.edu hg19 7 131912231 131912231 + Missense_Mutation SNP G G A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . PLXNA4 NM_020911 exon7 c.C1861T p.P621S TCCGGGGCACCTC . 46.0 21.0 115.0 0.0 . 873 . . Atlas-SNP RP1L1 94137 hgsc.bcm.edu hg19 8 10467732 10467732 + Missense_Mutation SNP T T A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . RP1L1 NM_178857 exon4 c.A3876T p.L1292F TTCAGCTAACTGC . 49.0 26.0 132.0 0.0 . 453 . . Atlas-SNP ZFHX4 79776 hgsc.bcm.edu hg19 8 77618337 77618337 + Missense_Mutation SNP G G A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 ZFHX4,NS,carcinoma,0,1 ZFHX4 NM_024721 exon2 c.G2014A p.G672S CCGGGTGGCTCTT . 52.0 8.0 96.0 0.0 . 878 . . Atlas-SNP GSDMC 56169 hgsc.bcm.edu hg19 8 130777987 130777987 + Missense_Mutation SNP C C G novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . GSDMC NM_031415 exon4 c.G457C p.D153H GGTTGTCCCCTCT . 53.0 18.0 110.0 0.0 . 71 . . Atlas-SNP VPS13A 23230 hgsc.bcm.edu hg19 9 79824389 79824389 + Nonsense_Mutation SNP C C T novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . VPS13A NM_001018038 exon6 c.C436T p.Q146X GTTACACAGATCA . 233.0 127.0 332.0 0.0 . 735 . . Atlas-SNP GRIN3A 116443 hgsc.bcm.edu hg19 9 104449365 104449365 + Missense_Mutation SNP C C A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . GRIN3A NM_133445 exon2 c.G817T p.D273Y TCCAGTCTTCCTG . 212.0 77.0 258.0 0.0 . 186 . . Atlas-SNP ADAMTSL2 9719 hgsc.bcm.edu hg19 9 136402628 136402628 + Silent SNP G G A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . ADAMTSL2 NM_014694 exon3 c.G192A p.G64G TTGCGGGGGTGGG . 60.0 25.0 115.0 0.0 . 40 . . Atlas-SNP AKR1C1 1645 hgsc.bcm.edu hg19 10 5009199 5009199 + Silent SNP T T C novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . AKR1C1 NM_001353 exon3 c.T333C p.V111V TTATGTTGACCTC . 311.0 137.0 347.0 0.0 . 39 . . Atlas-SNP ARMC3 219681 hgsc.bcm.edu hg19 10 23297251 23297251 + Silent SNP C C A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . ARMC3 NM_173081 exon15 c.C1876A p.R626R TATGGACGAAGTA . 138.0 21.0 151.0 0.0 . 102 . . Atlas-SNP MYO3A 53904 hgsc.bcm.edu hg19 10 26462898 26462898 + Silent SNP T T C novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . MYO3A NM_017433 exon30 c.T3705C p.A1235A GGAAGCTATGATC . 136.0 61.0 156.0 0.0 . 371 . . Atlas-SNP WAPAL 23063 hgsc.bcm.edu hg19 10 88206050 88206050 + Missense_Mutation SNP C C T novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . WAPAL NM_015045 exon16 c.G3271A p.E1091K TCTCTTCTGTACC . 180.0 104.0 261.0 0.0 . 81 . . Atlas-SNP IDE 3416 hgsc.bcm.edu hg19 10 94225544 94225544 + Missense_Mutation SNP T T C novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . IDE NM_004969 exon20 c.A2377G p.I793V AGTATATCTCGAT . 186.0 53.0 282.0 0.0 . 77 . . Atlas-SNP SLC39A13 91252 hgsc.bcm.edu hg19 11 47436693 47436693 + Missense_Mutation SNP G G T novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . SLC39A13 NM_001128225 exon9 c.G1023T p.L341F CCTCTTGGAAGAA . 127.0 48.0 136.0 0.0 . 18 . . Atlas-SNP ARHGEF12 23365 hgsc.bcm.edu hg19 11 120317715 120317715 + Missense_Mutation SNP G G C novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . ARHGEF12 NM_015313 exon18 c.G1510C p.E504Q GATGCAGAGCGAG . 143.0 42.0 217.0 0.0 . 133 . . Atlas-SNP RECQL 5965 hgsc.bcm.edu hg19 12 21643210 21643210 + Missense_Mutation SNP C C G novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . RECQL NM_032941 exon5 c.G317C p.G106A TCCTTTCCAGCCA . 94.0 88.0 175.0 0.0 . 45 . . Atlas-SNP PDZRN4 29951 hgsc.bcm.edu hg19 12 41967431 41967431 + Silent SNP G G T novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . PDZRN4 NM_001164595 exon10 c.G2850T p.L950L GCACCTGGTTAGG . 60.0 14.0 91.0 0.0 . 346 . . Atlas-SNP HOXC4 3221 hgsc.bcm.edu hg19 12 54447739 54447739 + Missense_Mutation SNP C C A rs377491433 alternate_allele TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . HOXC4 NM_014620 exon3 c.C33A p.N11K CTCTAACTACATC . 87.0 20.0 112.0 0.0 . 29 . . Atlas-SNP WIF1 11197 hgsc.bcm.edu hg19 12 65448938 65448938 + Missense_Mutation SNP G G C novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . WIF1 NM_007191 exon9 c.C978G p.C326W ACATTGGCATTTG . 95.0 24.0 149.0 0.0 . 96 . . Atlas-SNP FREM2 341640 hgsc.bcm.edu hg19 13 39357273 39357273 + Missense_Mutation SNP C C T novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . FREM2 NM_207361 exon5 c.C5708T p.P1903L TCATTCCCATCAG . 182.0 120.0 189.0 0.0 . 385 . . Atlas-SNP SYNE2 23224 hgsc.bcm.edu hg19 14 64518635 64518635 + Missense_Mutation SNP G G T novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . SYNE2 NM_182914 exon48 c.G8004T p.L2668F TGCCTTGACCACT . 252.0 126.0 291.0 0.0 . 577 . . Atlas-SNP TYRO3 7301 hgsc.bcm.edu hg19 15 41865515 41865515 + Silent SNP G G A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . TYRO3 NM_006293 exon17 c.G1995A p.E665E GGCAGAGGACATG . 62.0 12.0 115.0 0.0 . 169 . . Atlas-SNP SHC4 399694 hgsc.bcm.edu hg19 15 49148299 49148299 + Missense_Mutation SNP G G A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . SHC4 NM_203349 exon8 c.C1093T p.H365Y CGGCATGGCTATC . 123.0 37.0 163.0 0.0 . 70 . . Atlas-SNP MCTP2 55784 hgsc.bcm.edu hg19 15 94901825 94901825 + Missense_Mutation SNP G G C novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . MCTP2 NM_001159643 exon9 c.G1285C p.E429Q AAGCATGAGGAAC . 176.0 95.0 182.0 0.0 . 122 . . Atlas-SNP CHTF18 63922 hgsc.bcm.edu hg19 16 845334 845334 + Missense_Mutation SNP C C A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . CHTF18 NM_022092 exon16 c.C2153A p.T718N GGATCACCTTCCC . 52.0 27.0 48.0 0.0 . 52 . . Atlas-SNP TELO2 9894 hgsc.bcm.edu hg19 16 1551758 1551758 + Missense_Mutation SNP G G C novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . TELO2 NM_016111 exon11 c.G1456C p.D486H GGCTCTGACTCGG . 37.0 12.0 49.0 0.0 . 44 . . Atlas-SNP ITGAX 3687 hgsc.bcm.edu hg19 16 31372494 31372494 + Silent SNP T T C novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . ITGAX NM_000887 exon9 c.T972C p.D324D GAAAGATATTCAA . 96.0 65.0 128.0 0.0 . 198 . . Atlas-SNP DNAH9 1770 hgsc.bcm.edu hg19 17 11775087 11775087 + Missense_Mutation SNP A A T novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . DNAH9 NM_001372 exon52 c.A10226T p.Y3409F GGCCCTACCTGAG . 77.0 66.0 154.0 0.0 . 695 . . Atlas-SNP SLFN12 55106 hgsc.bcm.edu hg19 17 33749277 33749277 + Silent SNP G G T novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . SLFN12 NM_018042 exon2 c.C771A p.L257L GTCATCGAGGTCA . 167.0 60.0 122.0 0.0 . 56 . . Atlas-SNP NBR1 4077 hgsc.bcm.edu hg19 17 41345518 41345518 + Missense_Mutation SNP C C T novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . NBR1 NM_031862 exon12 c.C1387T p.H463Y CTTTCTCACAAAG . 227.0 32.0 181.0 0.0 . 55 . . Atlas-SNP SPATA20 64847 hgsc.bcm.edu hg19 17 48629417 48629417 + Silent SNP G G A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . SPATA20 NM_022827 exon14 c.G1833A p.A611A GAGTGCGTGGCTC . 248.0 81.0 223.0 0.0 . 59 . . Atlas-SNP LOC100653515 0 hgsc.bcm.edu hg19 17 76888033 76888033 + Missense_Mutation SNP C C A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . . NM_001243540 exon3 c.G553T p.G185C GCTGGCCCAACTC . 238.0 144.0 179.0 0.0 . . . . Atlas-SNP ANKRD12 23253 hgsc.bcm.edu hg19 18 9182491 9182491 + Missense_Mutation SNP A A G novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . ANKRD12 NM_001083625 exon2 c.A61G p.M21V AGCAATATGGTAG . 53.0 35.0 81.0 0.0 . 167 . . Atlas-SNP HRH4 59340 hgsc.bcm.edu hg19 18 22057509 22057509 + Silent SNP C C A rs115905515 bycluster;byfrequency;by1000genomes;alternate_allele TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . HRH4 NM_021624 exon3 c.C1156A p.R386R CACAGTCGGTCAG . 80.0 30.0 83.0 0.0 . 46 . C|0.998;T|0.002 Atlas-SNP DSC2 1824 hgsc.bcm.edu hg19 18 28650707 28650707 + Silent SNP A A T novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . DSC2 NM_024422 exon14 c.T2235A p.P745P ATCTCCAGGAGCT . 114.0 73.0 166.0 0.0 . 168 . . Atlas-SNP GAREM 64762 hgsc.bcm.edu hg19 18 29890226 29890226 + Missense_Mutation SNP C C A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 FAM59A,NS,adenocarcinoma,0,1 . NM_022751 exon3 c.G323T p.S108I TCCACACTGTTGA . 179.0 50.0 275.0 0.0 . . . . Atlas-SNP DTNA 1837 hgsc.bcm.edu hg19 18 32438291 32438291 + Silent SNP A A G novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . DTNA NM_001390 exon15 c.A1494G p.E498E GCATGAACAAGCT . 74.0 42.0 113.0 0.0 . 321 . . Atlas-SNP MALT1 10892 hgsc.bcm.edu hg19 18 56401614 56401614 + Splice_Site SNP G G A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . MALT1 NM_006785 exon12 c.1475+1G>A . TGCCACGTAAGAA . 117.0 73.0 198.0 0.0 . 55 . . Atlas-SNP PIGN 23556 hgsc.bcm.edu hg19 18 59768329 59768329 + Missense_Mutation SNP T T C novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . PIGN NM_176787 exon22 c.A2056G p.I686V TAATAATTTGATT . 56.0 37.0 81.0 0.0 . 62 . . Atlas-SNP ZNF729 100287226 hgsc.bcm.edu hg19 19 22499233 22499233 + Nonsense_Mutation SNP C C A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . ZNF729 NM_001242680 exon4 c.C3014A p.S1005X ATTCCTCAACCCT . 130.0 61.0 137.0 0.0 . 78 . . Atlas-SNP ZNF229 7772 hgsc.bcm.edu hg19 19 44934591 44934591 + Missense_Mutation SNP C C G novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . ZNF229 NM_014518 exon6 c.G365C p.C122S ACTCTACAGTCTT . 106.0 25.0 169.0 0.0 . 123 . . Atlas-SNP SYT3 84258 hgsc.bcm.edu hg19 19 51133064 51133064 + Missense_Mutation SNP G G T novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . SYT3 NM_032298 exon3 c.C1039A p.R347S TCTTGCGGTCAGG . 35.0 7.0 91.0 0.0 . 85 . . Atlas-SNP LILRA5 353514 hgsc.bcm.edu hg19 19 54823336 54823336 + Silent SNP C C A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . LILRA5 NM_181879 exon4 c.G207T p.G69G CAGGGTCCCCTGA . 204.0 122.0 297.0 1.0 . 49 . . Atlas-SNP LILRA1 11024 hgsc.bcm.edu hg19 19 55111991 55111991 + Missense_Mutation SNP C C A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . LILRA1 NM_006863 exon9 c.C1327A p.L443I AACACCCTCAGCC . 62.0 15.0 103.0 0.0 . 105 . . Atlas-SNP ERGIC3 51614 hgsc.bcm.edu hg19 20 34130635 34130635 + Missense_Mutation SNP C C A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . ERGIC3 NM_015966 exon4 c.C312A p.F104L CCTGTTCAAGCAA . 140.0 53.0 150.0 0.0 . 41 . . Atlas-SNP SLC12A5 57468 hgsc.bcm.edu hg19 20 44686186 44686186 + Missense_Mutation SNP T T G novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . SLC12A5 NM_001134771 exon26 c.T3362G p.L1121R AGCACCTGGACCG . 174.0 67.0 204.0 0.0 . 181 . . Atlas-SNP BACE2 25825 hgsc.bcm.edu hg19 21 42622762 42622762 + Silent SNP T T A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . BACE2 NM_138992 exon7 c.T1068A p.P356P CTTCCCTAAAATC . 209.0 96.0 218.0 0.0 . 45 . . Atlas-SNP CECR1 51816 hgsc.bcm.edu hg19 22 17662466 17662466 + Missense_Mutation SNP C C A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . CECR1 NM_017424 exon9 c.G1443T p.K481N ACTGTACCTGCAG . 121.0 62.0 164.0 0.0 . 77 . . Atlas-SNP PLA2G3 50487 hgsc.bcm.edu hg19 22 31533849 31533849 + Nonsense_Mutation SNP T T A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . PLA2G3 NM_015715 exon4 c.A913T p.K305X GCTGCTTCTGTCG . 189.0 101.0 304.0 0.0 . 85 . . Atlas-SNP TOM1 10043 hgsc.bcm.edu hg19 22 35717981 35717981 + Missense_Mutation SNP A A G novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . TOM1 NM_001135732 exon3 c.A167G p.K56R TAAAGAAGAGAAT . 71.0 24.0 104.0 0.0 . 43 . . Atlas-SNP ARMCX4 100131755 hgsc.bcm.edu hg19 X 100747169 100747169 + Missense_Mutation SNP G G T novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . ARMCX4 NM_001256155 exon2 c.G3593T p.S1198I AGACTAGTGAGGG . 9.0 7.0 3.0 0.0 . 2 . . Atlas-SNP IL1RAPL2 26280 hgsc.bcm.edu hg19 X 105011223 105011223 + Silent SNP T T C novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . IL1RAPL2 NM_017416 exon11 c.T1630C p.L544L AGCAAATTAAATT . 210.0 109.0 246.0 0.0 . 105 . . Atlas-SNP CUL4B 8450 hgsc.bcm.edu hg19 X 119669737 119669737 + Missense_Mutation SNP A A C novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . CUL4B NM_003588 exon18 c.T2162G p.L721R CACTGAAGTTTCC . 573.0 136.0 574.0 0.0 . 181 . . Atlas-SNP IDH3G 3421 hgsc.bcm.edu hg19 X 153055245 153055245 + Missense_Mutation SNP G G A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . IDH3G NM_004135 exon5 c.C268T p.H90Y TCACGTGCACCTC . 38.0 12.0 66.0 0.0 . 36 . . Atlas-SNP COX1 5742 hgsc.bcm.edu hg19 MT 6718 6718 + Missense_Mutation SNP G G A novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . . ENST00000361624 exon1 c.G815A p.G272D ACATAGGTATGGT . 151.0 9.0 575.0 0.0 . . . . Atlas-SNP COX1 5742 hgsc.bcm.edu hg19 MT 7074 7074 + Nonsense_Mutation SNP G G A rs9633436 TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . . ENST00000361624 exon1 c.G1171A p.G391X ATCATAGGAGGCT . 159.0 90.0 472.0 0.0 . . . . Atlas-SNP ND3 0 hgsc.bcm.edu hg19 MT 10401 10401 + Missense_Mutation SNP G G A rs28358278 bycluster;alternate_allele TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . . ENST00000361227 exon1 c.G343A p.E115K TGAACCGAATTGG . 167.0 7.0 623.0 0.0 . . . C|0.839;T|0.161 Atlas-SNP FOXD4L2 100036519 hgsc.bcm.edu hg19 9 42718188 42718189 + In_Frame_Ins INS - - GAG novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . FOXD4L2 NM_001099279 exon1 c.123_124insGAG p.D41delinsDE . . 390.0 46.0 566.0 0.0 . 4 . . Atlas-INDEL SAA1 6288 hgsc.bcm.edu hg19 11 18290820 18290820 + Frame_Shift_Del DEL G G - novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . SAA1 NM_199161 exon3 c.169delC p.R57fs . . 208.0 60.0 217.0 0.0 . 14 . . Atlas-Indel,Pindel FOXD4L2 100036519 hgsc.bcm.edu hg19 9 70428763 70428764 + In_Frame_Ins INS - - CCT novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . FOXD4L2 NM_001099279 exon1 c.137_138insAGG p.A46delinsEA . . 380.0 38.0 585.0 0.0 . 4 . . Atlas-INDEL ANXA13 312 hgsc.bcm.edu hg19 8 124701110 124701112 + Frame_Shift_Del DEL CCG CCG - novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 CCG CCG . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . ANXA13 NM_001003954 exon10 c.841_841del p.281_281del . . 114.0 16.0 184.0 0.0 . 38 . . Atlas-INDEL SAA2 6289 hgsc.bcm.edu hg19 11 18267513 18267513 + Frame_Shift_Del DEL C C - novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . SAA2 NM_030754 exon3 c.175delA p.N59fs . . 366.0 60.0 428.0 0.0 . 22 . . Atlas-Indel,Pindel CDH22 64405 hgsc.bcm.edu hg19 20 44856179 44856179 + Frame_Shift_Del DEL C C - novel TCGA-BC-A217-01A-11D-A152-10 TCGA-BC-A217-10A-01D-A152-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 2bff30d5-be79-4686-8164-7a7d9619d3c0 b12f2a60-b900-4c83-9b9e-d1f6bbd469f9 . CDH22 NM_021248 exon4 c.639delC p.G213fs . . 54.0 30.0 62.0 0.0 . 112 . . Atlas-Indel,Pindel