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 INADL 10207 hgsc.bcm.edu hg19 1 62330235 62330235 + Missense_Mutation SNP A A C novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . INADL NM_176877 exon20 c.A2765C p.Q922P AGTCTCAAGAGGC . 35.0 19.0 83.0 0.0 . 179 . . Atlas-SNP PTPN22 26191 hgsc.bcm.edu hg19 1 114380695 114380695 + Missense_Mutation SNP G G T novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . PTPN22 NM_015967 exon13 c.C1327A p.P443T TTATTGGCACCTT . 38.0 14.0 129.0 0.0 . 90 . . Atlas-SNP GJA8 2703 hgsc.bcm.edu hg19 1 147380863 147380863 + Nonsense_Mutation SNP C C T novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . GJA8 NM_005267 exon2 c.C781T p.Q261X TCCATCCAGAAAG . 66.0 31.0 74.0 0.0 . 108 . . Atlas-SNP GON4L 54856 hgsc.bcm.edu hg19 1 155723018 155723018 + Missense_Mutation SNP C C T novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . GON4L NM_001037533 exon29 c.G5819A p.R1940K CCCTTTCTGGTGG . 223.0 28.0 264.0 0.0 . 392 . . Atlas-SNP DUSP10 11221 hgsc.bcm.edu hg19 1 221912367 221912367 + Silent SNP G G A novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . DUSP10 NM_007207 exon2 c.C720T p.T240T TTCATTGGTATTC . 156.0 19.0 234.0 0.0 . 64 . . Atlas-SNP RYR2 6262 hgsc.bcm.edu hg19 1 237948157 237948157 + Missense_Mutation SNP T T A novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . RYR2 NM_001035 exon90 c.T13145A p.L4382Q TTGGCCTGGATCT . 77.0 23.0 84.0 0.0 . 1273 . . Atlas-SNP OR2T4 127074 hgsc.bcm.edu hg19 1 248525606 248525606 + Missense_Mutation SNP C C A novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . OR2T4 NM_001004696 exon1 c.C724A p.P242T CTCATCCCTGTGG . 1004.0 67.0 1155.0 0.0 . 126 . . Atlas-SNP OR2T6 254879 hgsc.bcm.edu hg19 1 248551626 248551626 + Silent SNP C C T rs148186126 TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b OR2T6,arm,malignant_melanoma,0,1 OR2T6 NM_001005471 exon1 c.C717T p.A239A CTTTGCCACCTGC . 310.0 86.0 307.0 0.0 . 101 . . Atlas-SNP OR2G6 391211 hgsc.bcm.edu hg19 1 248684959 248684959 + Silent SNP C C T novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b OR2G6,NS,carcinoma,0,1 OR2G6 NM_001013355 exon1 c.C12T p.T4T GGAAACCAACAAC . 215.0 74.0 250.0 0.0 . 124 . . Atlas-SNP OR2T10 127069 hgsc.bcm.edu hg19 1 248756794 248756794 + Silent SNP G G T novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . OR2T10 NM_001004693 exon1 c.C276A p.I92I GACCGAGATGGTC . 175.0 30.0 219.0 0.0 . 58 . . Atlas-SNP SMPD4 55627 hgsc.bcm.edu hg19 2 130930247 130930247 + Missense_Mutation SNP G G T novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . SMPD4 NM_017751 exon7 c.C575A p.P192Q TCGAACGGATCTG . 158.0 34.0 184.0 0.0 . 67 . . Atlas-SNP PLA2R1 22925 hgsc.bcm.edu hg19 2 160807990 160807990 + Missense_Mutation SNP G G T novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . PLA2R1 NM_001195641 exon24 c.C3401A p.T1134N TACCAAGTCATAT . 434.0 137.0 574.0 0.0 . 153 . . Atlas-SNP TRAF3IP1 26146 hgsc.bcm.edu hg19 2 239237694 239237694 + Missense_Mutation SNP G G T novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . TRAF3IP1 NM_015650 exon5 c.G626T p.G209V ATGGCGGAAACAG . 203.0 34.0 217.0 0.0 . 58 . . Atlas-SNP SEMA3F 6405 hgsc.bcm.edu hg19 3 50220186 50220186 + Silent SNP G G T novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . SEMA3F NM_004186 exon9 c.G873T p.A291A CCCCGCGGTGTAC . 24.0 11.0 47.0 0.0 . 62 . . Atlas-SNP MRPS22 56945 hgsc.bcm.edu hg19 3 139062905 139062905 + Missense_Mutation SNP C C T novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . MRPS22 NM_020191 exon1 c.C37T p.L13F TGGAGCCTCTTGA . 54.0 16.0 49.0 0.0 . 40 . . Atlas-SNP PLS1 5357 hgsc.bcm.edu hg19 3 142388293 142388293 + Silent SNP C C T novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . PLS1 NM_001172312 exon3 c.C132T p.S44S AGCAAGCCTTCCT . 79.0 9.0 107.0 0.0 . 71 . . Atlas-SNP EIF4G1 1981 hgsc.bcm.edu hg19 3 184039489 184039489 + Nonsense_Mutation SNP G G T novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . EIF4G1 NM_001194946 exon11 c.G1138T p.E380X GAACCAGAGGTGG . 135.0 21.0 163.0 0.0 . 151 . . Atlas-SNP PDE6B 5158 hgsc.bcm.edu hg19 4 651215 651215 + Missense_Mutation SNP A A G novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . PDE6B NM_001145291 exon10 c.A1333G p.K445E AACCGCAAGGACA . 192.0 32.0 173.0 0.0 . 80 . . Atlas-SNP CRMP1 1400 hgsc.bcm.edu hg19 4 5837733 5837733 + Missense_Mutation SNP C C T novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . CRMP1 NM_001014809 exon11 c.G1532A p.R511K CCTTTCCTTGGGT . 91.0 18.0 142.0 0.0 . 118 . . Atlas-SNP ATP8A1 10396 hgsc.bcm.edu hg19 4 42580401 42580401 + Missense_Mutation SNP C C T novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . ATP8A1 NM_001105529 exon12 c.G1004A p.G335D GCGCCACCATCTG . 91.0 14.0 117.0 0.0 . 206 . . Atlas-SNP PABPC4L 132430 hgsc.bcm.edu hg19 4 135121364 135121364 + Nonsense_Mutation SNP G G A novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . PABPC4L NM_001114734 exon2 c.C985T p.R329X CCTGTCGCTCGAC . 41.0 7.0 94.0 0.0 . 60 . . Atlas-SNP FAM134B 54463 hgsc.bcm.edu hg19 5 16474884 16474884 + Missense_Mutation SNP G G A novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . FAM134B NM_001034850 exon9 c.C1460T p.S487L AAACCTGAAGACT . 115.0 54.0 135.0 0.0 . 72 . . Atlas-SNP C5orf22 55322 hgsc.bcm.edu hg19 5 31534433 31534433 + Missense_Mutation SNP G G C novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . C5orf22 NM_018356 exon2 c.G136C p.V46L AGTAATGTAAGTT . 328.0 64.0 505.0 0.0 . 48 . . Atlas-SNP TMEM173 340061 hgsc.bcm.edu hg19 5 138855859 138855859 + Missense_Mutation SNP G G T rs370381358 alternate_allele TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . TMEM173 NM_198282 exon8 c.C1127A p.T376K AAATCCGTGCGGA . 67.0 31.0 116.0 0.0 . 19 . . Atlas-SNP PCDHA10 56139 hgsc.bcm.edu hg19 5 140237874 140237874 + Silent SNP T T C novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . PCDHA10 NM_031859 exon1 c.T2241C p.S747S CTGGTCTTACTCG . 134.0 29.0 285.0 0.0 . 358 . . Atlas-SNP PCDHGA5 56110 hgsc.bcm.edu hg19 5 140746244 140746244 + Missense_Mutation SNP G G A novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . PCDHGA5 NM_032054 exon1 c.G2347A p.E783K AGTGAAGAGAGCT . 81.0 16.0 161.0 0.0 . 215 . . Atlas-SNP HOXA4 3201 hgsc.bcm.edu hg19 7 27168891 27168891 + Missense_Mutation SNP G G A novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b HOXA4,NS,carcinoma,0,1 HOXA4 NM_002141 exon2 c.C916T p.P306S GGTGGGGATGGAG . 343.0 56.0 321.0 1.0 . 21 . . Atlas-SNP SEMA3D 223117 hgsc.bcm.edu hg19 7 84666319 84666319 + Silent SNP C C G rs143217112 alternate_allele TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . SEMA3D NM_152754 exon10 c.G1077C p.V359V GCTATACACACAA . 66.0 15.0 117.0 0.0 . 177 . C|1.000;T|0.000 Atlas-SNP ZSCAN25 221785 hgsc.bcm.edu hg19 7 99227217 99227217 + Silent SNP C C T novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . . NM_145115 exon8 c.C1209T p.Y403Y GCCCTACGTGTGC . 46.0 11.0 77.0 0.0 . . . . Atlas-SNP FLNC 2318 hgsc.bcm.edu hg19 7 128489494 128489494 + Silent SNP G G A novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . FLNC NM_001127487 exon30 c.G5061A p.G1687G GGATGGGGCAGAG . 73.0 10.0 94.0 0.0 . 339 . . Atlas-SNP CNOT4 4850 hgsc.bcm.edu hg19 7 135107050 135107050 + Missense_Mutation SNP T T C novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . CNOT4 NM_001190850 exon3 c.A227G p.Q76R ATCCTTTGCAGCT . 206.0 34.0 272.0 0.0 . 146 . . Atlas-SNP GSTK1 373156 hgsc.bcm.edu hg19 7 142964755 142964755 + Missense_Mutation SNP C C A novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . GSTK1 NM_001143679 exon5 c.C634A p.L212M GGACTTCTGGAAA . 108.0 42.0 103.0 0.0 . 36 . . Atlas-SNP CYP7A1 1581 hgsc.bcm.edu hg19 8 59409293 59409293 + Missense_Mutation SNP G G A novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . CYP7A1 NM_000780 exon3 c.C778T p.R260C ACATGCGCAGGCT . 172.0 41.0 203.0 0.0 . 76 . . Atlas-SNP FOXH1 8928 hgsc.bcm.edu hg19 8 145700607 145700607 + Missense_Mutation SNP C C A rs150426097 alternate_allele TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . FOXH1 NM_003923 exon2 c.G212T p.R71M TCTTCCCTGAAGA . 58.0 13.0 59.0 0.0 . 17 . C|1.000;T|0.000 Atlas-SNP IFNW1 3467 hgsc.bcm.edu hg19 9 21141286 21141286 + Missense_Mutation SNP C C A novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . IFNW1 NM_002177 exon1 c.G284T p.R95L GAGGAGCGCTCTG . 30.0 9.0 113.0 0.0 . 20 . . Atlas-SNP NOL6 65083 hgsc.bcm.edu hg19 9 33468831 33468831 + Missense_Mutation SNP C C G novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . NOL6 NM_022917 exon8 c.G1066C p.V356L AGACAACCAGCAT . 63.0 22.0 114.0 0.0 . 85 . . Atlas-SNP SFMBT2 57713 hgsc.bcm.edu hg19 10 7285628 7285628 + Silent SNP G G A novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . SFMBT2 NM_001029880 exon9 c.C1012T p.L338L GTCTTAGGTCATC . 104.0 11.0 93.0 0.0 . 209 . . Atlas-SNP MCM10 55388 hgsc.bcm.edu hg19 10 13212934 13212934 + Missense_Mutation SNP A A G novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . MCM10 NM_182751 exon3 c.A20G p.N7S AAGACAATCTGTC . 247.0 127.0 168.0 0.0 . 76 . . Atlas-SNP ANKRD30A 91074 hgsc.bcm.edu hg19 10 37505198 37505198 + Missense_Mutation SNP G G C novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b ANKRD30A_ENST00000602533,NS,carcinoma,-1,1 ANKRD30A NM_052997 exon32 c.G2791C p.G931R CGTACAGGAAAAA . 576.0 57.0 475.0 0.0 . 448 . . Atlas-SNP CDHR1 92211 hgsc.bcm.edu hg19 10 85955343 85955343 + Missense_Mutation SNP T T C novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . CDHR1 NM_001171971 exon2 c.T149C p.V50A CCCCTGTAGGTGA . 66.0 17.0 96.0 0.0 . 122 . . Atlas-SNP KNDC1 85442 hgsc.bcm.edu hg19 10 135025036 135025036 + Missense_Mutation SNP G G T rs151235501 alternate_allele TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . KNDC1 NM_152643 exon22 c.G4019T p.G1340V ACAGCGGGCTGCT . 65.0 23.0 74.0 0.0 . 155 . G|1.000;A|0.000 Atlas-SNP KCNA5 3741 hgsc.bcm.edu hg19 12 5154891 5154891 + Missense_Mutation SNP A A T novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . KCNA5 NM_002234 exon1 c.A1578T p.E526D CCGGGAAACGGAT . 64.0 14.0 114.0 0.0 . 138 . . Atlas-SNP RAPGEF3 10411 hgsc.bcm.edu hg19 12 48135289 48135289 + Missense_Mutation SNP A A G novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . RAPGEF3 NM_001098531 exon19 c.T1922C p.L641P CCTACCAGCTCAT . 143.0 30.0 141.0 0.0 . 98 . . Atlas-SNP OTOGL 283310 hgsc.bcm.edu hg19 12 80732951 80732951 + Missense_Mutation SNP G G A novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . OTOGL NM_173591 exon42 c.G4930A p.G1644R CCAGCTGGACTAA . 105.0 14.0 186.0 0.0 . 235 . . Atlas-SNP ACACB 32 hgsc.bcm.edu hg19 12 109637260 109637260 + Missense_Mutation SNP C C T novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . ACACB NM_001093 exon17 c.C2681T p.P894L ACGATCCTACAGT . 83.0 15.0 91.0 0.0 . 330 . . Atlas-SNP HPD 3242 hgsc.bcm.edu hg19 12 122284995 122284995 + Missense_Mutation SNP T T C novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . HPD NM_002150 exon10 c.A722G p.N241S GGCTCATTGATGG . 105.0 14.0 125.0 0.0 . 46 . . Atlas-SNP CENPJ 55835 hgsc.bcm.edu hg19 13 25459431 25459431 + Missense_Mutation SNP T T A novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . CENPJ NM_018451 exon13 c.A3460T p.S1154C GATGACTGATTTC . 115.0 31.0 258.0 0.0 . 116 . . Atlas-SNP TTC5 91875 hgsc.bcm.edu hg19 14 20763925 20763925 + Missense_Mutation SNP T T C novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . TTC5 NM_138376 exon7 c.A785G p.Q262R TCTCGTTGCCGGG . 106.0 18.0 138.0 0.0 . 34 . . Atlas-SNP MYH6 4624 hgsc.bcm.edu hg19 14 23851737 23851737 + Missense_Mutation SNP C C A rs61731171 bycluster;alternate_allele TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b MYH6,NS,carcinoma,0,1 MYH6 NM_002471 exon38 c.G5696T p.R1899L ACCTTGCGGAACT . 132.0 26.0 199.0 0.0 . 274 . C|0.986;T|0.014 Atlas-SNP UNC79 57578 hgsc.bcm.edu hg19 14 94052959 94052959 + Missense_Mutation SNP G G A novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b UNC79,NS,carcinoma,0,2 UNC79 NM_020818 exon21 c.G2290A p.E764K GATACCGAAAGAA . 69.0 19.0 208.0 0.0 . 366 . . Atlas-SNP TDRD9 122402 hgsc.bcm.edu hg19 14 104488538 104488538 + Missense_Mutation SNP C C T novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . TDRD9 NM_153046 exon24 c.C2477T p.T826I TTAAAACCCTTCC . 123.0 39.0 268.0 0.0 . 175 . . Atlas-SNP GABRA5 2558 hgsc.bcm.edu hg19 15 27114447 27114447 + Missense_Mutation SNP T T G novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b GABRA5,NS,carcinoma,0,1 GABRA5 NM_001165037 exon3 c.T52G p.F18V CTTCTCTTTTGTA . 234.0 48.0 409.0 1.0 . 127 . . Atlas-SNP TRPM1 4308 hgsc.bcm.edu hg19 15 31295063 31295063 + Silent SNP A A C novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . TRPM1 NM_001252020 exon27 c.T3891G p.L1297L CCGGAGAAGATAC . 82.0 17.0 138.0 0.0 . 183 . . Atlas-SNP RYR3 6263 hgsc.bcm.edu hg19 15 34105063 34105063 + Splice_Site SNP G G C novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . RYR3 NM_001243996 exon72 c.10243-1G>C . TTTTCAGTCTGAT . 56.0 11.0 87.0 0.0 . 760 . . Atlas-SNP INO80 54617 hgsc.bcm.edu hg19 15 41377743 41377743 + Missense_Mutation SNP C C T novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . INO80 NM_017553 exon7 c.G697A p.E233K GTTCTTCATCTCT . 315.0 62.0 548.0 0.0 . 122 . . Atlas-SNP CSPG4 1464 hgsc.bcm.edu hg19 15 75968322 75968322 + Missense_Mutation SNP C C T rs370893364 TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . CSPG4 NM_001897 exon10 c.G6538A p.E2180K CGGCCTCGGGGAC . 33.0 12.0 23.0 0.0 . 175 . . Atlas-SNP RPL13 6137 hgsc.bcm.edu hg19 16 89629361 89629361 + Missense_Mutation SNP C C T novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . RPL13 NM_000977 exon6 c.C547T p.R183C AGTCTCCGTATGG . 120.0 13.0 165.0 0.0 . 11 . . Atlas-SNP TP53 7157 hgsc.bcm.edu hg19 17 7578524 7578524 + Nonsense_Mutation SNP G G A novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b TP53_ENST00000545858,NS,carcinoma,0,4 TP53 NM_000546 exon5 c.C406T p.Q136X CCAGTTGGCAAAA . 35.0 21.0 48.0 0.0 . 33396 . . Atlas-SNP MYOCD 93649 hgsc.bcm.edu hg19 17 12666487 12666487 + Silent SNP C C T novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . MYOCD NM_001146312 exon14 c.C2487T p.P829P CAAGCCCTCGGCT . 56.0 34.0 121.0 0.0 . 291 . . Atlas-SNP MYO18A 399687 hgsc.bcm.edu hg19 17 27449219 27449219 + Missense_Mutation SNP T T G novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . MYO18A NM_078471 exon3 c.A1052C p.K351T CACACCTTCTCCG . 126.0 74.0 262.0 0.0 . 217 . . Atlas-SNP MED24 9862 hgsc.bcm.edu hg19 17 38189358 38189358 + Missense_Mutation SNP C C T novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . MED24 NM_014815 exon8 c.G773A p.G258D GTCTCGCCTGTCA . 37.0 18.0 87.0 0.0 . 89 . . Atlas-SNP MTMR4 9110 hgsc.bcm.edu hg19 17 56582147 56582147 + Missense_Mutation SNP G G A novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . MTMR4 NM_004687 exon12 c.C1292T p.T431M TCCAACGTCCTGT . 47.0 12.0 81.0 0.0 . 91 . . Atlas-SNP METTL2A 339175 hgsc.bcm.edu hg19 17 60501620 60501620 + Missense_Mutation SNP G G A novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . METTL2A NM_181725 exon2 c.G151A p.E51K GCGGCGGAGAGAA . 76.0 20.0 127.0 0.0 . 31 . . Atlas-SNP ENPP7 339221 hgsc.bcm.edu hg19 17 77711821 77711821 + Silent SNP G G A novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . ENPP7 NM_178543 exon5 c.G1353A p.V451V GACCGTGATTCTT . 38.0 16.0 43.0 0.0 . 63 . . Atlas-SNP SOCS6 9306 hgsc.bcm.edu hg19 18 67992724 67992724 + Missense_Mutation SNP G G C novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . SOCS6 NM_004232 exon2 c.G820C p.V274L GACCTAGTTGTCG . 164.0 55.0 279.0 0.0 . 54 . . Atlas-SNP C19orf21 126353 hgsc.bcm.edu hg19 19 756999 756999 + Missense_Mutation SNP G G C novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . C19orf21 NM_173481 exon2 c.G53C p.G18A ACCGTGGCACCGG . 116.0 15.0 113.0 0.0 . 56 . . Atlas-SNP PCSK4 54760 hgsc.bcm.edu hg19 19 1484101 1484101 + Missense_Mutation SNP C C T novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . PCSK4 NM_017573 exon9 c.G1094A p.C365Y TCTGTGCACCCGT . 128.0 71.0 68.0 0.0 . 44 . . Atlas-SNP SMARCA4 6597 hgsc.bcm.edu hg19 19 11143994 11143994 + Missense_Mutation SNP G G A novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b SMARCA4_ENST00000358026,NS,carcinoma,+1,2 SMARCA4 NM_003072 exon26 c.G3575A p.R1192H CCCACCGCATCGG . 77.0 15.0 90.0 0.0 . 502 . . Atlas-SNP C19orf80 55908 hgsc.bcm.edu hg19 19 11350899 11350899 + Missense_Mutation SNP G G T novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . C19orf80 NM_018687 exon2 c.G386T p.S129I GGGACAGCGTGCA . 65.0 26.0 89.0 0.0 . 8 . . Atlas-SNP SPTBN4 57731 hgsc.bcm.edu hg19 19 41073984 41073984 + Missense_Mutation SNP G G A novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . SPTBN4 NM_020971 exon31 c.G6752A p.R2251Q CTGAGCGGCAAGA . 50.0 15.0 41.0 0.0 . 213 . . Atlas-SNP PSG11 5680 hgsc.bcm.edu hg19 19 43529064 43529064 + Missense_Mutation SNP C C T novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . PSG11 NM_002785 exon2 c.G209A p.G70E ATTTGCCCTTTGT . 203.0 27.0 250.0 0.0 . 57 . . Atlas-SNP PSG9 5678 hgsc.bcm.edu hg19 19 43763032 43763032 + Missense_Mutation SNP T T G novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . PSG9 NM_002784 exon4 c.A965C p.N322T ACTGGGTTACTGC . 124.0 29.0 96.0 0.0 . 77 . . Atlas-SNP LMTK3 114783 hgsc.bcm.edu hg19 19 49013717 49013717 + Missense_Mutation SNP T T G novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . LMTK3 NM_001080434 exon3 c.A296C p.K99T CTCACCTTGAAGC . 125.0 19.0 143.0 0.0 . 125 . . Atlas-SNP TFPT 29844 hgsc.bcm.edu hg19 19 54611472 54611472 + Missense_Mutation SNP G G A novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . TFPT NM_013342 exon5 c.C503T p.P168L CTGGGCGGGGACA . 93.0 16.0 106.0 0.0 . 17 . . Atlas-SNP SIRPG 55423 hgsc.bcm.edu hg19 20 1629885 1629885 + Missense_Mutation SNP T T G novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . SIRPG NM_001039508 exon2 c.A243C p.K81N GCCTTCTTTTTGA . 816.0 294.0 1118.0 2.0 . 61 . . Atlas-SNP C20orf27 54976 hgsc.bcm.edu hg19 20 3735113 3735113 + Missense_Mutation SNP C C T novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . C20orf27 NM_001039140 exon5 c.G430A p.E144K GTATCTCCTCTTT . 83.0 30.0 61.0 0.0 . 17 . . Atlas-SNP RTFDC1 51507 hgsc.bcm.edu hg19 20 55048453 55048453 + Splice_Site SNP T T A novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . . NM_016407 exon2 c.164+2T>A . GGCAGGTATGGTT . 48.0 11.0 84.0 0.0 . . . . Atlas-SNP SYNJ1 8867 hgsc.bcm.edu hg19 21 34022586 34022586 + Missense_Mutation SNP C C T novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . SYNJ1 NM_203446 exon23 c.G3062A p.S1021N TCTAAACTCATTT . 237.0 77.0 406.0 0.0 . 253 . . Atlas-SNP MICAL3 57553 hgsc.bcm.edu hg19 22 18358243 18358243 + Silent SNP G G A rs201286172 TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . MICAL3 NM_001136004 exon19 c.C2475T p.P825P AGAGGCGGGGCGG . 59.0 12.0 73.0 0.0 . 53 . . Atlas-SNP TCF20 6942 hgsc.bcm.edu hg19 22 42606748 42606748 + Missense_Mutation SNP A A T novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . TCF20 NM_181492 exon1 c.T4564A p.S1522T TCGGTGAAATCGT . 323.0 22.0 352.0 0.0 . 164 . . Atlas-SNP SCML2 10389 hgsc.bcm.edu hg19 X 18283818 18283818 + Missense_Mutation SNP G G C novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . SCML2 NM_006089 exon8 c.C835G p.Q279E TGACCTGCTGTGT . 290.0 62.0 461.0 0.0 . 81 . . Atlas-SNP PHKA2 5256 hgsc.bcm.edu hg19 X 18972509 18972509 + Missense_Mutation SNP A A C novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . PHKA2 NM_000292 exon2 c.T100G p.S34A TGGCTGACAGCAG . 60.0 14.0 95.0 0.0 . 122 . . Atlas-SNP PRICKLE3 4007 hgsc.bcm.edu hg19 X 49032070 49032070 + Silent SNP G G A novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . PRICKLE3 NM_006150 exon9 c.C1800T p.R600R CCCTGCGCGAGAG . 94.0 19.0 102.0 0.0 . 59 . . Atlas-SNP SSX7 280658 hgsc.bcm.edu hg19 X 52677345 52677345 + Silent SNP T T C novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . SSX7 NM_173358 exon6 c.A432G p.K144K ACTTGGTTTTCCT . 1049.0 178.0 1399.0 1.0 . 34 . . Atlas-SNP KLF8 11279 hgsc.bcm.edu hg19 X 56291629 56291629 + Missense_Mutation SNP G G A rs144407506 bycluster TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . KLF8 NM_001159296 exon4 c.G98A p.R33Q CTGTTCGGAACAG . 108.0 17.0 175.0 0.0 . 38 . G|1.000;A|0.000 Atlas-SNP ABCD1 215 hgsc.bcm.edu hg19 X 153001604 153001604 + Missense_Mutation SNP G G C novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . ABCD1 NM_000033 exon3 c.G1120C p.E374Q AAGAAGGAGGAGG . 129.0 29.0 193.0 0.0 . 59 . . Atlas-SNP ND5 0 hgsc.bcm.edu hg19 MT 13718 13718 + Missense_Mutation SNP G G A novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . . ENST00000361567 exon1 c.G1382A p.S461N CCGGAAGCCTATT . 78.0 26.0 624.0 1.0 . . . . Atlas-SNP ND6 0 hgsc.bcm.edu hg19 MT 14607 14607 + Missense_Mutation SNP G G A novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . . ENST00000361681 exon1 c.C67T p.P23S GAGAAGGCTTAGA . 175.0 11.0 1100.0 0.0 . . . . Atlas-SNP CYTB 0 hgsc.bcm.edu hg19 MT 15357 15357 + Missense_Mutation SNP G G A novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . . ENST00000361789 exon1 c.G611A p.G204E AAACGGGATCAAA . 94.0 53.0 714.0 1.0 . . . . Atlas-SNP BAP1 8314 hgsc.bcm.edu hg19 3 52436687 52436688 + Frame_Shift_Ins INS - - A novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b BAP1,bladder,carcinoma,0,1 BAP1 NM_004656 exon16 c.1987_1988insT p.D663_D664delinsX . . 89.0 65.0 226.0 0.0 . 371 . . Atlas-Indel,Pindel GAB2 9846 hgsc.bcm.edu hg19 11 77937959 77937960 + Frame_Shift_Ins INS - - T novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . GAB2 NM_080491 exon4 c.759_760insA p.K253fs . . 77.0 13.0 123.0 0.0 . 63 . . Atlas-INDEL COMMD3-BMI1 0 hgsc.bcm.edu hg19 10 22606865 22606866 + Frame_Shift_Ins INS - - G novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . . NM_001204062 exon2 c.192_193insG p.A64fs . . 368.0 63.0 305.0 0.0 . . . . Atlas-Indel,Pindel PREX1 57580 hgsc.bcm.edu hg19 20 47307517 47307518 + Frame_Shift_Ins INS - - C novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . PREX1 NM_020820 exon9 c.1154_1155insG p.D385fs . . 161.0 10.0 185.0 0.0 . 441 . . Atlas-INDEL REXO1 57455 hgsc.bcm.edu hg19 19 1828274 1828275 + Frame_Shift_Ins INS - - G novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . REXO1 NM_020695 exon2 c.514_515insC p.A172fs . . 51.0 11.0 58.0 0.0 . 55 . . Atlas-INDEL DHX36 170506 hgsc.bcm.edu hg19 3 154042059 154042060 + Frame_Shift_Ins INS - - C novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . DHX36 NM_020865 exon1 c.147_148insG p.G49fs . . 244.0 15.0 223.0 0.0 . 98 . . Atlas-INDEL ATP9B 374868 hgsc.bcm.edu hg19 18 77108133 77108134 + Frame_Shift_Ins INS - - TG novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . ATP9B NM_198531 exon25 c.2840_2841insTG p.A947fs . . 242.0 63.0 392.0 0.0 . 96 . . Atlas-Indel,Pindel OTOP1 133060 hgsc.bcm.edu hg19 4 4199089 4199090 + Frame_Shift_Ins INS - - G novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . OTOP1 NM_177998 exon5 c.1472_1473insC p.Q491fs . . 157.0 13.0 219.0 0.0 . 118 . . Atlas-INDEL CPXM1 56265 hgsc.bcm.edu hg19 20 2776314 2776315 + Frame_Shift_Ins INS - - G novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . CPXM1 NM_019609 exon11 c.1651_1652insC p.C551fs . . 137.0 13.0 123.0 0.0 . 107 . . Atlas-INDEL LARP4B 23185 hgsc.bcm.edu hg19 10 858938 858939 + Frame_Shift_Ins INS - - C novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b .,1 LARP4B NM_015155 exon18 c.2145_2146insG p.G715fs . . 129.0 12.0 66.0 0.0 . 110 . . Atlas-INDEL LGALS14 56891 hgsc.bcm.edu hg19 19 40196577 40196757 + Frame_Shift_Del DEL CAAGTACTGGGGCTGTGCTGTCAGTAATGTGTGCCGCTTCTGGGAAGGACGTCCATTGCCCTTGATGATTGTGGTGCGTGTACATCCCACACACAGGGGTTTCCTGTTCTTTCGTCATTTCCCTTTCTCTTTCAACAAGTGTTGTTTCTCACTGGAGTGAATTTTTAAATTCTTTCACCCT CAAGTACTGGGGCTGTGCTGTCAGTAATGTGTGCCGCTTCTGGGAAGGACGTCCATTGCCCTTGATGATTGTGGTGCGTGTACATCCCACACACAGGGGTTTCCTGTTCTTTCGTCATTTCCCTTTCTCTTTCAACAAGTGTTGTTTCTCACTGGAGTGAATTTTTAAATTCTTTCACCCT - novel TCGA-BC-A10R-01A-11D-A12Z-10 TCGA-BC-A10R-11A-11D-A12Z-10 CAAGTACTGGGGCTGTGCTGTCAGTAATGTGTGCCGCTTCTGGGAAGGACGTCCATTGCCCTTGATGATTGTGGTGCGTGTACATCCCACACACAGGGGTTTCCTGTTCTTTCGTCATTTCCCTTTCTCTTTCAACAAGTGTTGTTTCTCACTGGAGTGAATTTTTAAATTCTTTCACCCT CAAGTACTGGGGCTGTGCTGTCAGTAATGTGTGCCGCTTCTGGGAAGGACGTCCATTGCCCTTGATGATTGTGGTGCGTGTACATCCCACACACAGGGGTTTCCTGTTCTTTCGTCATTTCCCTTTCTCTTTCAACAAGTGTTGTTTCTCACTGGAGTGAATTTTTAAATTCTTTCACCCT . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e98ae9b4-4696-4b17-a6ed-b072d679ba40 a458c859-a526-4bd8-a5ff-ed71b5ce571b . LGALS14 NM_203471 exon2 c.29_102del p.10_34del . . 106.0 10.0 171.0 0.0 . 38 . . Pindel