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 TranscriptID Exon ChromChange AAChange Genome_Plus_Minus_10_Bp Drug_Target TTotCov TVarCov NTotCov NVarCov dbSNPPopFreq COSMIC_Gene_Freq ABLIM2 84448 ucsc.edu;bcgsc.ca 37 4 7968764 7968764 + Missense_Mutation SNP C C T novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic . WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . ABLIM2 NM_001130083 exon21 c.G1891A p.A631T AGAGGGCCAGGCG . 30.0 4.0 41.0 0.0 . 47 ACSBG1 23205 hgsc.bcm.edu;broad.mit.edu;bcgsc.ca 37 15 78472115 78472136 + Frame_Shift_Del DEL TCAGGTCGCTGGTGGGAGAGGG TCAGGTCGCTGGTGGGAGAGGG - novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 TCAGGTCGCTGGTGGGAGAGGG TCAGGTCGCTGGTGGGAGAGGG . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . ACSBG1 NM_015162 exon10 c.1254_1261del p.418_421del AGGGCTTCAGGTC . 162.0 14.0 125.0 0.0 . 91 AFF2 2334 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 X 147744245 147744245 + Missense_Mutation SNP T T A novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 T T . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . AFF2 NM_002025 exon3 c.T997A p.S333T GCCAGTTCAAAGA . 309.0 288.0 357.0 1.0 . 135 APBA2 321 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 15 29346830 29346830 + Missense_Mutation SNP C C T novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . APBA2 NM_005503 exon3 c.C743T p.A248V GTGAGGCCAGCCC . 134.0 60.0 126.0 0.0 . 90 ATP13A1 57130 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 19 19756558 19756558 + Silent SNP C C T novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . ATP13A1 NM_020410 exon25 c.G3402A p.L1134L CCACACCAGGGGC . 85.0 53.0 81.0 0.0 . 138 ATP13A1 57130 ucsc.edu;bcgsc.ca 37 19 19763412 19763412 + Missense_Mutation SNP A A G novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic . WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . ATP13A1 NM_020410 exon16 c.T2218C p.S740P GGTGGGACGCATT . 39.0 5.0 66.0 1.0 . 138 ATP2C2 9914 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;mdanderson.org 37 16 84486812 84486812 + Nonsense_Mutation SNP A A T novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . ATP2C2 NM_014861 exon19 c.A1900T p.K634X GTGGAGAAGGGCG . 115.0 49.0 111.0 0.0 . 91 ATP5B 506 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 12 57032145 57032145 + Missense_Mutation SNP C C T novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . ATP5B NM_001686 exon10 c.G1552A p.A518T CTTTTGCCACAGC . 146.0 55.0 147.0 0.0 . 91 ATP8A2 51761 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 13 26153014 26153014 + Missense_Mutation SNP A A G novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . ATP8A2 NM_016529 exon21 c.A1844G p.H615R TATGCCATCTGGA . 89.0 38.0 111.0 0.0 . 138 BAI2 576 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 1 32196897 32196897 + Missense_Mutation SNP A A T novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . BAI2 NM_001703 exon29 c.T3884A p.F1295Y GGTGAGAAGCTGA . 175.0 85.0 163.0 0.0 . 526 BRCA2 675 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca 37 13 32914712 32914712 + Missense_Mutation SNP C C G rs34309943 byfrequency;alternate_allele TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . BRCA2 NM_000059 exon11 c.C6220G p.H2074D TCCTTACACAAAG . 94.0 38.0 127.0 0.0 C|0.998;A|0.002 3153 BRSK1 84446 ucsc.edu;bcgsc.ca 37 19 55805701 55805701 + Missense_Mutation SNP A A G novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic . WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . BRSK1 NM_032430 exon7 c.A614G p.E205G AGGGGGAAAAATA . 39.0 4.0 77.0 0.0 . 759 CACNA1H 8912 ucsc.edu;bcgsc.ca 37 16 1270989 1270989 + Missense_Mutation SNP G G A rs150601404 TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic . WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . CACNA1H NM_021098 exon35 c.G7057A p.V2353M GACCCCGTGTAGC . 46.0 4.0 53.0 0.0 G|0.998;A|0.002 67 CCDC88C 440193 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 14 91770248 91770248 + Silent SNP C C T novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . CCDC88C NM_001080414 exon20 c.G3432A p.T1144T CTTGGCCGTGTGG . 130.0 51.0 100.0 0.0 . 25 COL16A1 1307 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 1 32162651 32162651 + Missense_Mutation SNP C C G novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . COL16A1 NM_001856 exon8 c.G777C p.Q259H ATTGCTCTGGGTG . 305.0 136.0 273.0 0.0 . 98 COTL1 23406 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 16 84623756 84623756 + Silent SNP G G A novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . COTL1 NM_021149 exon3 c.C273T p.R91R TTTGGCGCGCTGC . 139.0 67.0 120.0 0.0 . 226 CTNNA2 1496 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 2 80085161 80085161 + Silent SNP C C T novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . CTNNA2 NM_001164883 exon4 c.C321T p.S107S CGCCTCCTCCGAG . 128.0 52.0 136.0 0.0 . 368 CXCR6 10663 broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 3 45988614 45988614 + Missense_Mutation SNP T T C novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 T T . . . . . Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . CXCR6 NM_006564 exon2 c.T641C p.I214T CAGTCATAATCAA . 216.0 88.0 219.0 1.0 . 658 DCLK1 9201 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;mdanderson.org 37 13 36385025 36385025 + Nonsense_Mutation SNP G G T novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . DCLK1 NM_004734 exon12 c.C1635A p.Y545X GACTGTGTACAGG . 252.0 110.0 202.0 0.0 . 826 DPP10 57628 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 2 116510776 116510776 + Missense_Mutation SNP G G T novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . DPP10 NM_001178034 exon11 c.G989T p.W330L TTAAATGGGTAAG . 196.0 73.0 299.0 0.0 . 142 ECH1 1891 broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 19 39322054 39322054 + Missense_Mutation SNP T T C novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 T T . . . . . Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . ECH1 NM_001398 exon2 c.A155G p.D52G CTGTGGTCTGGGG . 60.0 27.0 62.0 1.0 . 91 EIF2S3 1968 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 X 24084190 24084190 + Missense_Mutation SNP T T C novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 T T . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . EIF2S3 NM_001415 exon8 c.T848C p.I283T GTAGTATCCTAAA . 387.0 346.0 480.0 0.0 . 130 EVPL 2125 broad.mit.edu;bcgsc.ca 37 17 74003349 74003349 + Silent SNP C C T novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 C C . . . . . Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . EVPL NM_001988 exon22 c.G5937A p.E1979E ATCCTTCTCGTAG . 210.0 11.0 142.0 0.0 . 93 EXOSC10 5394 ucsc.edu;bcgsc.ca 37 1 11158092 11158092 + Missense_Mutation SNP T T C novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 T T . . . . Unknown Untested Somatic . WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . EXOSC10 NM_002685 exon2 c.A233G p.D78G AACCTGTCTCCCT . 48.0 4.0 49.0 0.0 . 116 G6PC 2538 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 17 41063222 41063222 + Missense_Mutation SNP A A G novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . G6PC NM_000151 exon5 c.A853G p.K285E AGCTGCAAGGGGA . 177.0 74.0 155.0 0.0 . 292 GDF5 8200 broad.mit.edu;mdanderson.org 37 20 34022500 34022500 + Missense_Mutation SNP T T A novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 T T . . . . . Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . GDF5 NM_000557 exon2 c.A713T p.E238V CGCAGCTCGGCCC . 19.0 7.0 9.0 0.0 . 226 GH1 2688 hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org 37 17 61994712 61994712 + Missense_Mutation SNP C C T novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . GH1 NM_000515 exon5 c.G611A p.R204H ACGATGCGCAGGA . 611.0 163.0 413.0 1.0 . 522 GPHN 10243 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 14 67646366 67646366 + Missense_Mutation SNP A A T novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . GPHN NM_020806 exon22 c.A2151T p.E717D CCAAGAACCACTA . 300.0 139.0 329.0 0.0 . 228 GPSM1 26086 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 9 139234260 139234260 + Silent SNP G G A novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . GPSM1 NM_015597 exon8 c.G1071A p.Q357Q CCTGCAGATCTCC . 105.0 30.0 86.0 0.0 . 90 HSPA12A 259217 ucsc.edu;bcgsc.ca 37 10 118451933 118451933 + Missense_Mutation SNP T T C novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 T T . . . . Unknown Untested Somatic . WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . HSPA12A NM_025015 exon6 c.A592G p.R198G CCCATCTGACATC . 48.0 4.0 68.0 0.0 . 206 ICAM1 3383 hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org 37 19 10385686 10385686 + Missense_Mutation SNP A A G novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . ICAM1 NM_000201 exon2 c.A313G p.T105A GCTAAAACCTTCC . 55.0 31.0 77.0 0.0 . 91 INSR 3643 broad.mit.edu;bcgsc.ca 37 19 7143085 7143085 + Missense_Mutation SNP T T C novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 T T . . . . . Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . INSR NM_000208 exon12 c.A2284G p.R762G GGGACCTGCGTTT . 55.0 6.0 44.0 0.0 . 1381 ISPD 729920 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 7 16298092 16298092 + Missense_Mutation SNP A A T rs199890239 TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . ISPD NM_001101426 exon8 c.T1042A p.F348I CTTGAAAATCAGA . 101.0 37.0 94.0 0.0 A|0.999;T|0.001 23 JMJD1C 221037 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 10 64952867 64952867 + Silent SNP G G A novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . JMJD1C NM_032776 exon16 c.C5907T p.C1969C AGGCATGCACAGA . 144.0 63.0 165.0 0.0 . 275 KHSRP 8570 broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 19 6420136 6420136 + Silent SNP T T C novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 T T . . . . . Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . KHSRP NM_003685 exon6 c.A495G p.E165E AATTTGTTCACCT . 136.0 53.0 185.0 1.0 . 226 KIF1C 10749 ucsc.edu;bcgsc.ca 37 17 4926003 4926003 + Missense_Mutation SNP A A G novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic . WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . KIF1C NM_006612 exon22 c.A2627G p.Q876R TGGCCCAGGTAGG . 20.0 4.0 19.0 0.0 . 92 KNDC1 85442 broad.mit.edu;bcgsc.ca 37 10 135033549 135033549 + Missense_Mutation SNP C C T novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 C C . . . . . Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . KNDC1 NM_152643 exon29 c.C4951T p.H1651Y GCCATGCACATCC . 87.0 6.0 182.0 0.0 . 229 KRT8 3856 ucsc.edu;bcgsc.ca 37 12 53294400 53294400 + Missense_Mutation SNP A A G novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic . WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . KRT8 NM_001256282 exon5 c.T746C p.I249T AAGTTGATCTCGT . 41.0 5.0 51.0 0.0 . 92 LAMB4 22798 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 7 107688358 107688358 + Missense_Mutation SNP T T C novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 T T . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . LAMB4 NM_007356 exon28 c.A4321G p.N1441D CCTGATTTTTCAA . 354.0 168.0 374.0 0.0 . 140 LCE1E 353135 broad.mit.edu;bcgsc.ca 37 1 152759943 152759944 + Frame_Shift_Ins INS - - GTGGA novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 - - . . . . . Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . LCE1E NM_178353 exon2 c.168_169insGTGGA p.S56fs CAGCTCTGGGGGC . 293.0 0.0 173.0 0.0 . 90 LHX8 431707 hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org 37 1 75602325 75602325 + Missense_Mutation SNP C C T novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . LHX8 NM_001001933 exon3 c.C56T p.T19I GGACTACAGCCCT . 73.0 34.0 74.0 0.0 . 93 LOC81691 0 broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 16 20826252 20826252 + Missense_Mutation SNP G G T rs201728796 alternate_allele TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 G G . . . . . Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . LOC81691 NM_030941 exon4 c.G255T p.W85C CAGCTGGTGCCAG . 184.0 76.0 211.0 0.0 G|0.999;A|0.000 92 MAB21L1 4081 hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org 37 13 36049710 36049710 + Missense_Mutation SNP A A G novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . MAB21L1 NM_005584 exon1 c.T566C p.L189P TGGGGAAGTGGCC . 55.0 23.0 96.0 0.0 . 92 MAN1B1 11253 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 9 140001761 140001761 + Silent SNP C C T novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . MAN1B1 NM_016219 exon11 c.C1626T p.P542P CCTGCCCGCCAGC . 263.0 89.0 162.0 0.0 . 91 MAP3K15 389840 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 X 19410152 19410152 + Missense_Mutation SNP G G A novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . MAP3K15 NM_001001671 exon18 c.C2399T p.A800V ACACCCGCAAGAC . 49.0 44.0 36.0 0.0 . 335 MAZ 4150 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 16 29820038 29820038 + Missense_Mutation SNP C C T novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . MAZ NM_002383 exon4 c.C1255T p.H419Y CCTCACCATGTCT . 85.0 36.0 104.0 0.0 . 136 METTL9 51108 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 16 21636425 21636425 + Missense_Mutation SNP A A G novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . METTL9 NM_016025 exon4 c.A740G p.Y247C ATCCCTATGTGGA . 139.0 46.0 169.0 0.0 . 91 MLL3 58508 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 7 151873592 151873592 + Silent SNP A A C novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . MLL3 NM_170606 exon38 c.T8946G p.V2982V AGAAAAAACATGG . 187.0 76.0 191.0 0.0 . 1398 MYBPC1 4604 broad.mit.edu;bcgsc.ca 37 12 102067254 102067254 + Missense_Mutation SNP A A T novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 A A . . . . . Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . MYBPC1 NM_206819 exon25 c.A2663T p.D888V AAATTGATAAGAA . 138.0 6.0 156.0 1.0 . 94 NAPSA 9476 broad.mit.edu;bcgsc.ca 37 19 50864210 50864210 + Missense_Mutation SNP A A G novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 A A . . . . . Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . NAPSA NM_004851 exon5 c.T656C p.F219S AGGTAAAAGGAGA . 82.0 7.0 115.0 0.0 . 90 NID2 22795 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 14 52520942 52520942 + Missense_Mutation SNP C C T rs200644684 TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . NID2 NM_007361 exon4 c.G865A p.A289T GGGCAGCGGAAAG . 82.0 33.0 75.0 0.0 C|0.999;T|0.000 158 NIPAL4 348938 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 5 156899886 156899886 + Missense_Mutation SNP A A G novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . NIPAL4 NM_001099287 exon6 c.A1319G p.K440R AAGACAAGAACGT . 82.0 34.0 80.0 0.0 . 68 NIPBL 25836 broad.mit.edu;bcgsc.ca 37 5 36976272 36976272 + Silent SNP G G A novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 G G . . . . . Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . NIPBL NM_015384 exon9 c.G1263A p.S421S TTTGTCGCAGCAA . 172.0 7.0 187.0 0.0 . 293 NRCAM 4897 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 7 107866734 107866734 + Silent SNP G G A novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . NRCAM NM_001037132 exon6 c.C639T p.R213R GTCTTCGCGGGTG . 47.0 21.0 62.0 0.0 . 156 OR1J2 26740 broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 9 125273978 125273978 + Missense_Mutation SNP G G A novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 G G . . . . . Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . OR1J2 NM_054107 exon1 c.G898A p.A300T AAAGAGGCCCTTG . 152.0 59.0 169.0 2.0 . 72 OR4M1 441670 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca 37 14 20249191 20249191 + Missense_Mutation SNP G G A novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . OR4M1 NM_001005500 exon1 c.G710A p.R237K CCAACAGGGCCAT . 693.0 279.0 701.0 0.0 . 68 PCDH11Y 83259 hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org 37 Y 4925278 4925278 + Silent SNP C C T novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . . NM_032972 exon1 c.C414T p.C138C GCATTGCTTTTAT . 684.0 496.0 736.0 1.0 . . PCLO 27445 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 7 82464992 82464992 + Missense_Mutation SNP T T C novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 T T . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . PCLO NM_014510 exon16 c.A14240G p.Q4747R GCATTCTGGACAA . 180.0 84.0 162.0 0.0 . 29 PDGFA 5154 hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org 37 7 550578 550578 + Silent SNP C C T novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . PDGFA NM_002607 exon4 c.G321A p.R107R CTGACTCCGAGGA . 137.0 63.0 93.0 0.0 . 454 PELI2 57161 ucsc.edu;bcgsc.ca 37 14 56746414 56746414 + Silent SNP A A G novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic . WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . PELI2 NM_021255 exon3 c.A228G p.Q76Q AGGTCAACACAGT . 47.0 4.0 53.0 0.0 . 91 PHRF1 57661 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 11 608299 608299 + Missense_Mutation SNP C C T rs200183606 TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . PHRF1 NM_020901 exon14 c.C2840T p.S947F GGGCGTCTTGCAG . 34.0 14.0 21.0 0.0 C|0.996;T|0.004 22 PIGF 5281 hgsc.bcm.edu;ucsc.edu;bcgsc.ca 37 2 46839477 46839477 + Silent SNP T T A rs1824050 byfrequency;alternate_allele TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 T T . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . PIGF NM_002643 exon4 c.A327T p.A109A TTCCAATGCCAAC . 323.0 152.0 502.0 2.0 T|0.797;C|0.203 226 PLCXD2 257068 broad.mit.edu;bcgsc.ca;mdanderson.org 37 3 111432938 111432938 + Missense_Mutation SNP G G T novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 G G . . . . . Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . PLCXD2 NM_001185106 exon3 c.G829T p.G277C GCCCGGGGCTTGG . 68.0 33.0 48.0 1.0 . 227 PLD3 23646 ucsc.edu;bcgsc.ca 37 19 40880392 40880392 + Missense_Mutation SNP C C T novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic . WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . PLD3 NM_012268 exon10 c.C884T p.A295V AGAGTGCGCCCCC . 38.0 4.0 76.0 0.0 . 228 POGZ 23126 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 1 151414583 151414583 + Missense_Mutation SNP T T C novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 T T . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . POGZ NM_145796 exon2 c.A98G p.Y33C GAATTATAATCTT . 265.0 87.0 207.0 0.0 . 93 POLE2 5427 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 14 50140883 50140883 + Silent SNP A A G novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . POLE2 NM_001197331 exon5 c.T375C p.D125D TGCTTTATCTCTT . 167.0 78.0 182.0 0.0 . 229 PROC 5624 ucsc.edu;bcgsc.ca 37 2 128184733 128184733 + Missense_Mutation SNP A A G novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic . WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . PROC NM_000312 exon8 c.A731G p.H244R TCATCCACCCCTC . 53.0 6.0 42.0 0.0 . 90 PTCH1 5727 hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org 37 9 98268744 98268744 + Silent SNP C C A novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . PTCH1 NM_000264 exon2 c.G339T p.A113A TCCCACCGCGAAG . 200.0 90.0 181.0 0.0 . 3532 RABL6 55684 hgsc.bcm.edu;broad.mit.edu;bcgsc.ca 37 9 139732077 139732077 + Silent SNP G G A novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . . NM_001173988 exon9 c.G1092A p.G364G GTTTGGGACGTCA . 82.0 24.0 32.0 0.0 . . RHO 6010 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 3 129252455 129252455 + Missense_Mutation SNP G G A novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . RHO NM_000539 exon5 c.G941A p.R314Q AGTTCCGGAACTG . 68.0 33.0 33.0 0.0 . 90 RRBP1 6238 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 20 17596122 17596122 + Missense_Mutation SNP G G A novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . RRBP1 NM_004587 exon23 c.C2705T p.A902V GGGCCGGCTGTGC . 99.0 43.0 97.0 0.0 . 92 RRP1B 23076 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 21 45092191 45092191 + Silent SNP A A G novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . RRP1B NM_015056 exon3 c.A216G p.E72E GCAGGAAGAGCTC . 118.0 54.0 139.0 0.0 . 91 SEMA7A 8482 broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 15 74709733 74709733 + Missense_Mutation SNP G G A novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 G G . . . . . Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . SEMA7A NM_003612 exon6 c.C604T p.R202W GGAACCGAGGGAT . 208.0 45.0 127.0 1.0 . 153 SERPINB6 5269 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 6 2959566 2959566 + Missense_Mutation SNP T T C novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 T T . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . SERPINB6 NM_001271823 exon2 c.A58G p.M20V CATCCATGATGGC . 155.0 65.0 130.0 0.0 . 226 SLIT3 6586 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 5 168119629 168119629 + Silent SNP G G A novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . SLIT3 NM_001271946 exon29 c.C3180T p.P1060P GTCCAGGGGGATG . 90.0 9.0 73.0 0.0 . 95 SND1 27044 broad.mit.edu;bcgsc.ca 37 7 127528038 127528038 + Missense_Mutation SNP A A G novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 A A . . . . . Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . SND1 NM_014390 exon13 c.A1427G p.Y476C CACACTACGATGA . 90.0 5.0 87.0 0.0 . 92 SNTG2 54221 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 2 1079315 1079315 + Missense_Mutation SNP G G T novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . SNTG2 NM_018968 exon2 c.G184T p.V62L GTCTGTGTGGGCG . 90.0 36.0 110.0 0.0 . 136 ST8SIA2 8128 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 15 93007604 93007604 + Missense_Mutation SNP G G T rs149476731 TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . ST8SIA2 NM_006011 exon6 c.G1117T p.G373W TGCGATGGGGCCA . 86.0 26.0 45.0 0.0 G|1.000;T|0.000 90 TH 7054 broad.mit.edu;bcgsc.ca 37 11 2185482 2185482 + Missense_Mutation SNP G G A rs201219944 TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 G G . . . . . Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . TH NM_199292 exon14 c.C1568T p.A523V CTCAGCGCATGGG . 61.0 4.0 64.0 0.0 G|0.996;A|0.005 90 TRPM6 140803 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 9 77416900 77416900 + Silent SNP C C T novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . TRPM6 NM_017662 exon16 c.G1923A p.A641A GATACACGCAATC . 192.0 84.0 168.0 0.0 . 335 UGT2B15 7366 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 4 69535667 69535667 + Missense_Mutation SNP A A G novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 A A . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . UGT2B15 NM_001076 exon1 c.T670C p.W224R GAAACCAAAAGTC . 184.0 147.0 429.0 2.0 . 46 ULK2 9706 broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 17 19705133 19705133 + Missense_Mutation SNP C C A novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 C C . . . . . Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . ULK2 NM_001142610 exon16 c.G1398T p.R466S GGAGAGCCTTCGT . 176.0 64.0 132.0 1.0 . 334 UPK1B 7348 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;mdanderson.org 37 3 118909118 118909118 + Nonsense_Mutation SNP T T A rs113148509 alternate_allele TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 T T . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . UPK1B NM_006952 exon4 c.T297A p.Y99X AGTATATGCCTTT . 443.0 178.0 523.0 0.0 T|0.500;C|0.500 90 USH2A 7399 broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 1 216496858 216496858 + Missense_Mutation SNP C C T novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 C C . . . . . Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . USH2A NM_007123 exon8 c.G1508A p.R503K CTGTGTCTGAGGT . 359.0 104.0 217.0 1.0 . 115 VRK2 7444 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 2 58373591 58373591 + Missense_Mutation SNP G G C novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . VRK2 NM_001130480 exon12 c.G1164C p.M388I ATTGATGAACAAT . 343.0 145.0 402.0 0.0 . 334 WDR87 83889 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 19 38383656 38383656 + Missense_Mutation SNP G G A novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 G G . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . . NM_031951 exon4 c.C2570T p.T857I CTGTAGGTTACAT . 373.0 182.0 315.0 1.0 . . YTHDF3 253943 broad.mit.edu;ucsc.edu;mdanderson.org 37 8 64099147 64099147 + Missense_Mutation SNP G G T novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 G G . . . . . Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . . . . . . TGACTGGACTGAA . 166.0 67.0 174.0 0.0 . . ZHX2 22882 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 8 123965265 123965265 + Silent SNP C C A novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . ZHX2 NM_014943 exon3 c.C1515A p.S505S CGAATCCCTTGCC . 40.0 17.0 31.0 0.0 . 227 ZNF445 353274 hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org 37 3 44489484 44489484 + Missense_Mutation SNP C C A novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . ZNF445 NM_181489 exon8 c.G1679T p.R560L GTTTCTCGGTGCA . 92.0 12.0 114.0 0.0 . 91 ZNF785 146540 hgsc.bcm.edu;broad.mit.edu;bcgsc.ca 37 16 30594358 30594358 + Frame_Shift_Del DEL C C - novel TCGA-BC-A10Y-01A-11D-A12Z-10 TCGA-BC-A10Y-11A-11D-A12Z-10 C C . . . . Unknown Untested Somatic Phase_I WXS none . . Illumina HiSeq 54f8357c-9dd7-4e08-bd47-a1ebedb30b62 5589b608-e6ae-4953-8a37-484d4116179b . ZNF785 NM_152458 exon3 c.741delG p.R247fs AGCCCGCCTGTGG . 70.0 31.0 68.0 0.0 . 91