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 ref_context gc_content t_alt_count t_ref_count PTEN 5728 hgsc.bcm.edu;broad.mit.edu;ucsc.edu 37 10 89711899 89711899 + Missense_Mutation SNP C C T rs121913293 TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db CAGTCAGAGGCGCTATGTGTA 0.348 73 51 NUP160 23279 hgsc.bcm.edu;broad.mit.edu;ucsc.edu 37 11 47809761 47809761 + Missense_Mutation SNP G G A TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db AAAGACTGGCGTTAAGGGAAG 0.398 30 45 PTPN11 5781 hgsc.bcm.edu;broad.mit.edu;ucsc.edu 37 12 112888199 112888199 + Missense_Mutation SNP C C A rs121918454 TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db GAGAAATTTGCCACTTTGGCT 0.418 74 120 SIPA1L1 26037 hgsc.bcm.edu;broad.mit.edu;ucsc.edu 37 14 72138006 72138006 + Missense_Mutation SNP G G A TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db ACTCGGACCCGCCAGGAATAC 0.473 29 51 NPAP1 23742 hgsc.bcm.edu;broad.mit.edu;ucsc.edu 37 15 24921561 24921561 + Missense_Mutation SNP G G A rs151186438 byFrequency TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db CCTTAGCAGCGGAGAAGCATC 0.597 20 27 ATP8B4 79895 hgsc.bcm.edu;broad.mit.edu;ucsc.edu 37 15 50288937 50288937 + Missense_Mutation SNP G G A rs116334504 by1000genomes TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db AGTGCATGGCGGACTTTTAGG 0.398 22 48 TMEM170A 124491 hgsc.bcm.edu;broad.mit.edu;ucsc.edu 37 16 75481522 75481522 + Silent SNP T T G TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db CAGTGCCCAGTGTGAGGGCTT 0.408 65 113 LAMA1 284217 hgsc.bcm.edu;broad.mit.edu;ucsc.edu 37 18 6961754 6961754 + Missense_Mutation SNP A A G TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db AACACTCCGGATGGGCTGGAC 0.517 14 27 AC010336.1 0 hgsc.bcm.edu;broad.mit.edu;ucsc.edu 37 19 7964897 7964897 + Missense_Mutation SNP G G A TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db GAGGAGCTCCGCGAGGTGCCG 0.657 10 22 ZNF229 7772 hgsc.bcm.edu;broad.mit.edu;ucsc.edu 37 19 44933647 44933647 + Missense_Mutation SNP C C T TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db TTGCCACACTCGCTGCAGGTG 0.537 31 59 HIF3A 64344 hgsc.bcm.edu;broad.mit.edu;ucsc.edu 37 19 46800337 46800337 + Missense_Mutation SNP G G A TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db GCGAGCCATGGCGCTGGGGCT 0.716 13 26 SZT2 23334 hgsc.bcm.edu;ucsc.edu 37 1 43888908 43888908 + Missense_Mutation SNP G G A TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db GTCACCCCCCGTGCTGGGGCC 0.617 18 26 USP24 23358 hgsc.bcm.edu;broad.mit.edu;ucsc.edu 37 1 55638164 55638164 + Nonsense_Mutation SNP C C T TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db TTTCAGTACCCCACTTGTGAA 0.368 22 73 CD1A 909 hgsc.bcm.edu;broad.mit.edu;ucsc.edu 37 1 158226760 158226760 + Silent SNP C C T TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db GGTATCTCCGCGCAACCCTGG 0.632 66 95 OBSCN 84033 hgsc.bcm.edu;broad.mit.edu;ucsc.edu 37 1 228431148 228431148 + Missense_Mutation SNP T T C TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db TCCTTCCGCCTGCACATCACA 0.547 11 16 ANKEF1 63926 hgsc.bcm.edu;broad.mit.edu;ucsc.edu 37 20 10030224 10030224 + Missense_Mutation SNP G G A TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db TCCGTAGAACGTGAGGCTTTC 0.512 44 99 PCSK2 5126 hgsc.bcm.edu;broad.mit.edu;ucsc.edu 37 20 17410117 17410117 + Missense_Mutation SNP G G A TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db TTCTGCTGCCGCCAACAACAA 0.473 110 308 MAP3K19 80122 hgsc.bcm.edu;broad.mit.edu;ucsc.edu 37 2 135745373 135745373 + Nonsense_Mutation SNP G G A TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db TCAGGTTTTCGCGTTTTACTA 0.378 50 69 COL6A3 1293 hgsc.bcm.edu;broad.mit.edu;ucsc.edu 37 2 238249727 238249727 + Missense_Mutation SNP G G A rs114806654 by1000genomes TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db GCTCCCTGCCGCTCTCCTGTC 0.512 106 179 SEMA3F 6405 hgsc.bcm.edu;broad.mit.edu 37 3 50225347 50225347 + Silent SNP C C T TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db CACCCCCAGGCGCAGGCCCCC 0.667 11 15 PDE6B 5158 hgsc.bcm.edu;broad.mit.edu;ucsc.edu 37 4 647918 647918 + Missense_Mutation SNP C C T TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db CAGCCGTACTCGGGCCCACGC 0.647 31 69 EDNRA 1909 hgsc.bcm.edu;broad.mit.edu;ucsc.edu 37 4 148407184 148407184 + Silent SNP G G T TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db GCCCCAACGCGCTGATAGCCA 0.423 70 91 TRIP13 9319 hgsc.bcm.edu;broad.mit.edu;ucsc.edu 37 5 908507 908507 + Missense_Mutation SNP C C T TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db GCCTGCAGGGCGGGCACCGAG 0.562 49 69 ATP10B 23120 hgsc.bcm.edu;broad.mit.edu;ucsc.edu 37 5 160025790 160025790 + Missense_Mutation SNP C C A TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db AGAGTTCTGGCCACTCTTGTA 0.502 195 286 PKHD1 5314 hgsc.bcm.edu;broad.mit.edu;ucsc.edu 37 6 51613287 51613287 + Missense_Mutation SNP C C A TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db GTGCCAAACACAATATTGTCA 0.493 46 45 PKHD1 5314 hgsc.bcm.edu;broad.mit.edu;ucsc.edu 37 6 51892973 51892973 + Missense_Mutation SNP C C A TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db TGAATGCTGACCCCATTGATA 0.498 124 213 COL19A1 1310 hgsc.bcm.edu;broad.mit.edu;ucsc.edu 37 6 70866054 70866054 + Silent SNP G G A TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db GTGTCCCAGGGCTGAAAAGCA 0.473 39 50 CALN1 83698 hgsc.bcm.edu;broad.mit.edu;ucsc.edu 37 7 71252834 71252834 + Missense_Mutation SNP C C T TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db ATAGCAAAGGCGCATATGAGG 0.567 27 80 ADAM7 8756 hgsc.bcm.edu;broad.mit.edu;ucsc.edu 37 8 24346749 24346749 + Missense_Mutation SNP T T G TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db CCAACATGCATGCTCAACATT 0.398 49 72 FER1L6 654463 hgsc.bcm.edu;broad.mit.edu 37 8 125094698 125094698 + Splice_Site SNP A A T TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db CCAGTATGAGATGTAAGTTCT 0.512 63 110 TRPM6 140803 hgsc.bcm.edu;broad.mit.edu;ucsc.edu 37 9 77377508 77377508 + Missense_Mutation SNP G G T TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db AGGCAAGACAGTTTCTGCTGA 0.507 104 160 OR13C5 138799 hgsc.bcm.edu;broad.mit.edu 37 9 107361264 107361264 + Missense_Mutation SNP A A C TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db CCCAGCTGCCATGGGTACATA 0.473 24 338 SVEP1 79987 hgsc.bcm.edu;broad.mit.edu;ucsc.edu 37 9 113217968 113217968 + Missense_Mutation SNP G G C TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db ATCGATGTCTGTTTCACACTT 0.418 20 33 RGN 9104 hgsc.bcm.edu;broad.mit.edu;ucsc.edu 37 X 46943843 46943843 + Missense_Mutation SNP C C T TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db CGTGGCTCTTCGCCAGTCGGG 0.493 18 5 TENM1 10178 hgsc.bcm.edu;broad.mit.edu;ucsc.edu 37 X 123654451 123654451 + Missense_Mutation SNP C C T TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db TTAATTGCGGCGGGAAACCAC 0.473 114 25 CARD14 79092 broad.mit.edu;ucsc.edu 37 17 78171904 78171904 + Missense_Mutation SNP C C T TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db CCAGACCTTCCGCAGCTGGAA 0.592 27 103 SUPT16H 11198 broad.mit.edu;ucsc.edu 37 14 21821703 21821703 + Missense_Mutation SNP C C T TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db TTCTTCACTACCCAATGACTC 0.373 52 107 DDR2 4921 broad.mit.edu;ucsc.edu 37 1 162741843 162741843 + Missense_Mutation SNP C C T TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db GCCAGTCCAGCCCAGTGGCCC 0.577 11 15 SLC30A6 55676 broad.mit.edu;hgsc.bcm.edu 37 2 32422896 32422896 + Splice_Site DEL G G - TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db TTGAAATTAAGTGAGTATTTT 0.373 47 91 PLCG1 5335 broad.mit.edu;hgsc.bcm.edu 37 20 39802386 39802387 + In_Frame_Ins INS - - GAAGAA TCGA-CS-5395-01A-01D-1468-08 TCGA-CS-5395-10A-01D-1468-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3d477ac1-3bdf-4410-9594-1a3a1412c6ae baa7b05c-d0b5-4b1c-b4fa-8955abe5c3db TGGTGTATGAGGAAGACATGTT 0.515 47 228