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 dataset type classification start end gene chr ref_allele tum_allele1 tum_allele2 context NBPF1 55672 broad.mit.edu 36 1 16780516 16780516 + Silent SNP T T C novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 16780516 16780516 NBPF1 1 T T C 52 UBR4 23352 broad.mit.edu 36 1 19316315 19316316 + Nonsense_Mutation DNP CC CC AT novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation DNP 19316315 19316316 UBR4 1 CC CC AT 30 E2F2 1870 broad.mit.edu 36 1 23720971 23720971 + Missense_Mutation SNP C C T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 23720971 23720971 E2F2 1 C C T 19 GPATCH4 54865 broad.mit.edu 36 1 154835451 154835451 + Silent SNP G G A novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 154835451 154835451 GPATCH4 1 G G A 43 CUBN 8029 broad.mit.edu 36 10 16951724 16951724 + Missense_Mutation SNP C C T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 16951724 16951724 CUBN 10 C C T 28 YME1L1 10730 broad.mit.edu 36 10 27465289 27465289 + Missense_Mutation SNP C C G novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 27465289 27465289 YME1L1 10 C C G 29 ANKRD30A 91074 broad.mit.edu 36 10 37491772 37491772 + Silent SNP A A T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 37491772 37491772 ANKRD30A 10 A A T 8 ANK3 288 broad.mit.edu 36 10 61637875 61637875 + Silent SNP C C T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 61637875 61637875 ANK3 10 C C T 21 PLCE1 51196 broad.mit.edu 36 10 95996007 95996007 + Missense_Mutation SNP A A G novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 95996007 95996007 PLCE1 10 A A G 4 SLIT1 6585 broad.mit.edu 36 10 98806955 98806955 + Splice_Site_SNP SNP A A C novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 98806955 98806955 SLIT1 10 A A C 14 NRAP 4892 broad.mit.edu 36 10 115367224 115367224 + Missense_Mutation SNP T T C novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 115367224 115367224 NRAP 10 T T C 53 MRPL23 6150 broad.mit.edu 36 11 1928740 1928740 + Missense_Mutation SNP G G C novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 1928740 1928740 MRPL23 11 G G C 39 TRIM6-TRIM34 53840 broad.mit.edu 36 11 5610315 5610315 + Missense_Mutation SNP G G C novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 5610315 5610315 TRIM6-TRIM34 11 G G C 47 OR5P2 120065 broad.mit.edu 36 11 7774842 7774842 + Missense_Mutation SNP G G T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 7774842 7774842 OR5P2 11 G G T 43 HPS5 11234 broad.mit.edu 36 11 18261972 18261972 + Missense_Mutation SNP C C T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 18261972 18261972 HPS5 11 C C T 26 KCNA4 3739 broad.mit.edu 36 11 29990600 29990600 + Missense_Mutation SNP G G C novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 29990600 29990600 KCNA4 11 G G C 40 RAG1 5896 broad.mit.edu 36 11 36554336 36554336 + Missense_Mutation SNP A A C novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 36554336 36554336 RAG1 11 A A C 1 PRPF19 27339 broad.mit.edu 36 11 60425396 60425396 + Nonsense_Mutation SNP C C A novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 60425396 60425396 PRPF19 11 C C A 30 NUMA1 4926 broad.mit.edu 36 11 71402374 71402374 + Missense_Mutation SNP C C T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 71402374 71402374 NUMA1 11 C C T 32 NUMA1 4926 broad.mit.edu 36 11 71403242 71403242 + Silent SNP C C A novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 71403242 71403242 NUMA1 11 C C A 22 OR6X1 390260 broad.mit.edu 36 11 123129939 123129939 + Silent SNP G G A novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 123129939 123129939 OR6X1 11 G G A 33 PKNOX2 63876 broad.mit.edu 36 11 124805219 124805219 + Silent SNP G G A novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 124805219 124805219 PKNOX2 11 G G A 35 CCDC77 84318 broad.mit.edu 36 12 420055 420055 + Silent SNP T T C novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 420055 420055 CCDC77 12 T T C 49 WNK1 378465 broad.mit.edu 36 12 848090 848090 + Silent SNP A A G novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 848090 848090 WNK1 12 A A G 11 KRT78 196374 broad.mit.edu 36 12 51524660 51524660 + Nonsense_Mutation SNP C C A novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 51524660 51524660 KRT78 12 C C A 30 EP400 57634 broad.mit.edu 36 12 131063515 131063515 + Silent SNP C C T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 131063515 131063515 EP400 12 C C T 23 BRCA2 675 broad.mit.edu 36 13 31812137 31812137 + Nonsense_Mutation SNP C C A novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 31812137 31812137 BRCA2 13 C C A 29 SLC39A2 29986 broad.mit.edu 36 14 20537526 20537526 + Silent SNP C C T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 20537526 20537526 SLC39A2 14 C C T 32 LRRC16B 90668 broad.mit.edu 36 14 23595742 23595742 + Missense_Mutation SNP G G C novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 23595742 23595742 LRRC16B 14 G G C 46 LRFN5 145581 broad.mit.edu 36 14 41443117 41443117 + Nonsense_Mutation SNP G G T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 41443117 41443117 LRFN5 14 G G T 41 GOLGA5 9950 broad.mit.edu 36 14 92352454 92352454 + Missense_Mutation SNP G G C novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 92352454 92352454 GOLGA5 14 G G C 33 TMED3 23423 broad.mit.edu 36 15 77393308 77393308 + Missense_Mutation SNP C C A novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 77393308 77393308 TMED3 15 C C A 18 MPG 4350 broad.mit.edu 36 16 75510 75510 + Missense_Mutation SNP G G T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 75510 75510 MPG 16 G G T 41 GPR97 222487 broad.mit.edu 36 16 56275888 56275888 + Silent SNP T T C novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 56275888 56275888 GPR97 16 T T C 54 CDH5 1003 broad.mit.edu 36 16 64970832 64970832 + Missense_Mutation SNP G G A novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 64970832 64970832 CDH5 16 G G A 46 COG8 84342 broad.mit.edu 36 16 67930898 67930898 + Missense_Mutation SNP T T A novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 67930898 67930898 COG8 16 T T A 54 TAF1C 9013 broad.mit.edu 36 16 82770694 82770694 + Missense_Mutation SNP G G A novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 82770694 82770694 TAF1C 16 G G A 46 PLD2 5338 broad.mit.edu 36 17 4658070 4658070 + Silent SNP C C T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 4658070 4658070 PLD2 17 C C T 19 ZBTB4 57659 broad.mit.edu 36 17 7307108 7307108 + Silent SNP G G A novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 7307108 7307108 ZBTB4 17 G G A 40 TP53 7157 broad.mit.edu 36 17 7518236 7518236 + Missense_Mutation SNP A A T rs28934577 Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 7518236 7518236 TP53 17 A A T 7 MYH2 4620 broad.mit.edu 36 17 10383329 10383329 + Missense_Mutation SNP C C T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 10383329 10383329 MYH2 17 C C T 27 SGCA 6442 broad.mit.edu 36 17 45600918 45600918 + Missense_Mutation SNP G G C novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 45600918 45600918 SGCA 17 G G C 35 ABCA5 23461 broad.mit.edu 36 17 64763521 64763521 + Silent SNP T T A novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 64763521 64763521 ABCA5 17 T T A 63 SLC25A23 79085 broad.mit.edu 36 19 6405349 6405349 + Missense_Mutation SNP G G T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 6405349 6405349 SLC25A23 19 G G T 45 OR7D4 125958 broad.mit.edu 36 19 9186271 9186271 + Missense_Mutation SNP C C T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 9186271 9186271 OR7D4 19 C C T 25 NOTCH3 4854 broad.mit.edu 36 19 15161209 15161209 + Missense_Mutation SNP A A G novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 15161209 15161209 NOTCH3 19 A A G 10 BST2 684 broad.mit.edu 36 19 17376202 17376202 + Missense_Mutation SNP T T G novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 17376202 17376202 BST2 19 T T G 64 CD22 933 broad.mit.edu 36 19 40520738 40520738 + Missense_Mutation SNP C C T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 40520738 40520738 CD22 19 C C T 31 CD22 933 broad.mit.edu 36 19 40528449 40528449 + Missense_Mutation SNP C C G novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 40528449 40528449 CD22 19 C C G 17 ZFP112 7771 broad.mit.edu 36 19 49523684 49523684 + Silent SNP T T C novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 49523684 49523684 ZFP112 19 T T C 55 BCL3 602 broad.mit.edu 36 19 49954678 49954678 + Missense_Mutation SNP C C A novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 49954678 49954678 BCL3 19 C C A 23 GRIN2D 2906 broad.mit.edu 36 19 53609175 53609175 + Splice_Site_SNP SNP G G C novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 53609175 53609175 GRIN2D 19 G G C 44 SNTG2 54221 broad.mit.edu 36 2 1069341 1069341 + Missense_Mutation SNP T T A novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 1069341 1069341 SNTG2 2 T T A 51 LHCGR 3973 broad.mit.edu 36 2 48768695 48768695 + Missense_Mutation SNP A A G novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 48768695 48768695 LHCGR 2 A A G 8 USP34 9736 broad.mit.edu 36 2 61346784 61346784 + Missense_Mutation SNP T T A novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 61346784 61346784 USP34 2 T T A 52 C2orf86 51057 broad.mit.edu 36 2 63485059 63485059 + Missense_Mutation SNP C C A novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 63485059 63485059 C2orf86 2 C C A 22 MAT2A 4144 broad.mit.edu 36 2 85623357 85623358 + Silent DNP TC TC AT novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Silent DNP 85623357 85623358 MAT2A 2 TC TC AT 58 MARCO 8685 broad.mit.edu 36 2 119456295 119456295 + Missense_Mutation SNP G G T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 119456295 119456295 MARCO 2 G G T 37 MGAT5 4249 broad.mit.edu 36 2 134728478 134728478 + Nonsense_Mutation SNP C C T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 134728478 134728478 MGAT5 2 C C T 29 SCN3A 6328 broad.mit.edu 36 2 165655606 165655606 + Missense_Mutation SNP G G C novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 165655606 165655606 SCN3A 2 G G C 38 TTN 7273 broad.mit.edu 36 2 179308659 179308659 + Missense_Mutation SNP G G A novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 179308659 179308659 TTN 2 G G A 40 PTH2R 5746 broad.mit.edu 36 2 209066555 209066555 + Missense_Mutation SNP G G C novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 209066555 209066555 PTH2R 2 G G C 41 MAP2 4133 broad.mit.edu 36 2 210267648 210267648 + Missense_Mutation SNP G G C novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 210267648 210267648 MAP2 2 G G C 33 USP37 57695 broad.mit.edu 36 2 219032778 219032778 + Silent SNP C C T rs71415835 Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 219032778 219032778 USP37 2 C C T 24 ASB18 401036 broad.mit.edu 36 2 236814733 236814733 + Missense_Mutation SNP T T G novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 236814733 236814733 ASB18 2 T T G 60 C20orf12 55184 broad.mit.edu 36 20 18377628 18377628 + Missense_Mutation SNP T T C novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 18377628 18377628 C20orf12 20 T T C 56 BPIL1 80341 broad.mit.edu 36 20 31064363 31064363 + Missense_Mutation SNP C C G novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 31064363 31064363 BPIL1 20 C C G 29 SLC7A4 6545 broad.mit.edu 36 22 19714504 19714504 + Silent SNP C C G novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 19714504 19714504 SLC7A4 22 C C G 19 KBTBD5 131377 broad.mit.edu 36 3 42702426 42702426 + Missense_Mutation SNP G G T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 42702426 42702426 KBTBD5 3 G G T 48 CCR3 1232 broad.mit.edu 36 3 46281819 46281819 + Missense_Mutation SNP G G T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 46281819 46281819 CCR3 3 G G T 44 HYAL3 8372 broad.mit.edu 36 3 50307982 50307982 + Missense_Mutation SNP C C T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 50307982 50307982 HYAL3 3 C C T 17 GRK7 131890 broad.mit.edu 36 3 143009181 143009181 + Missense_Mutation SNP G G C novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 143009181 143009181 GRK7 3 G G C 41 WDR49 151790 broad.mit.edu 36 3 168737372 168737372 + Missense_Mutation SNP G G T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 168737372 168737372 WDR49 3 G G T 35 TP63 8626 broad.mit.edu 36 3 190939252 190939252 + Missense_Mutation SNP A A T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 190939252 190939252 TP63 3 A A T 8 FAT4 79633 broad.mit.edu 36 4 126461302 126461302 + Missense_Mutation SNP T T C novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 126461302 126461302 FAT4 4 T T C 52 IQGAP2 10788 broad.mit.edu 36 5 76024953 76024953 + Missense_Mutation SNP T T C novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 76024953 76024953 IQGAP2 5 T T C 52 PCDHA2 56146 broad.mit.edu 36 5 140155966 140155966 + Silent SNP C C T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 140155966 140155966 PCDHA2 5 C C T 27 FBXO38 81545 broad.mit.edu 36 5 147787703 147787703 + Missense_Mutation SNP G G C novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 147787703 147787703 FBXO38 5 G G C 35 LARP1 23367 broad.mit.edu 36 5 154163167 154163167 + Splice_Site_SNP SNP G G T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 154163167 154163167 LARP1 5 G G T 44 HLA-DRA 3122 broad.mit.edu 36 6 32518414 32518414 + Missense_Mutation SNP G G A novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 32518414 32518414 HLA-DRA 6 G G A 45 ANKS1A 23294 broad.mit.edu 36 6 35159259 35159259 + Splice_Site_SNP SNP G G C novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 35159259 35159259 ANKS1A 6 G G C 44 GLO1 2739 broad.mit.edu 36 6 38778750 38778750 + Missense_Mutation SNP C C T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 38778750 38778750 GLO1 6 C C T 25 GLO1 2739 broad.mit.edu 36 6 38778781 38778781 + Missense_Mutation SNP C C A novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 38778781 38778781 GLO1 6 C C A 23 TCTE1 202500 broad.mit.edu 36 6 44358180 44358180 + Missense_Mutation SNP A A C novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 44358180 44358180 TCTE1 6 A A C 5 SUPT3H 8464 broad.mit.edu 36 6 45079481 45079481 + Missense_Mutation SNP T T C novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 45079481 45079481 SUPT3H 6 T T C 62 GCLC 2729 broad.mit.edu 36 6 53481376 53481376 + Silent SNP T T C novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 53481376 53481376 GCLC 6 T T C 62 KIAA1244 57221 broad.mit.edu 36 6 138572856 138572856 + Missense_Mutation SNP G G T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 138572856 138572856 KIAA1244 6 G G T 35 TULP4 56995 broad.mit.edu 36 6 158830742 158830742 + Missense_Mutation SNP A A G novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 158830742 158830742 TULP4 6 A A G 5 WIPF3 644150 broad.mit.edu 36 7 29882023 29882023 + Missense_Mutation SNP C C T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 29882023 29882023 WIPF3 7 C C T 27 ELMO1 9844 broad.mit.edu 36 7 37265361 37265361 + Silent SNP T T A novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 37265361 37265361 ELMO1 7 T T A 61 AMPH 273 broad.mit.edu 36 7 38472374 38472374 + Splice_Site_SNP SNP C C T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 38472374 38472374 AMPH 7 C C T 32 EGFR 1956 broad.mit.edu 36 7 55191120 55191120 + Silent SNP G G A novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 55191120 55191120 EGFR 7 G G A 42 MAGI2 9863 broad.mit.edu 36 7 78474351 78474351 + Missense_Mutation SNP T T G novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 78474351 78474351 MAGI2 7 T T G 59 SEMA3A 10371 broad.mit.edu 36 7 83602188 83602188 + Missense_Mutation SNP T T A novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 83602188 83602188 SEMA3A 7 T T A 60 PPP1R3A 5506 broad.mit.edu 36 7 113346029 113346029 + Missense_Mutation SNP T T C novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 113346029 113346029 PPP1R3A 7 T T C 54 UBXN2B 137886 broad.mit.edu 36 8 59521102 59521102 + Missense_Mutation SNP G G A novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 59521102 59521102 UBXN2B 8 G G A 45 VPS13B 157680 broad.mit.edu 36 8 100956946 100956946 + Missense_Mutation SNP C C A novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 100956946 100956946 VPS13B 8 C C A 28 CHRAC1 54108 broad.mit.edu 36 8 141590861 141590861 + Silent SNP C C A novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 141590861 141590861 CHRAC1 8 C C A 29 C8orf31 286122 broad.mit.edu 36 8 144196018 144196018 + Silent SNP C C G novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 144196018 144196018 C8orf31 8 C C G 24 FLJ46321 389763 broad.mit.edu 36 9 83797393 83797393 + Missense_Mutation SNP G G C novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 83797393 83797393 FLJ46321 9 G G C 47 GRIN3A 116443 broad.mit.edu 36 9 103472336 103472336 + Silent SNP A A G novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 103472336 103472336 GRIN3A 9 A A G 3 TUBB2C 10383 broad.mit.edu 36 9 139257713 139257713 + Missense_Mutation SNP T T A novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 139257713 139257713 TUBB2C 9 T T A 60 WWC3 55841 broad.mit.edu 36 X 10022214 10022214 + Missense_Mutation SNP G G A novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 10022214 10022214 WWC3 23 G G A 40 ELK1 2002 broad.mit.edu 36 X 47383596 47383596 + Missense_Mutation SNP C C A novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 47383596 47383596 ELK1 23 C C A 25 HUWE1 10075 broad.mit.edu 36 X 53624524 53624524 + Nonsense_Mutation SNP G G C novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 53624524 53624524 HUWE1 23 G G C 45 NONO 4841 broad.mit.edu 36 X 70428478 70428478 + Silent SNP A A C novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 70428478 70428478 NONO 23 A A C 16 PHKA1 5255 broad.mit.edu 36 X 71772949 71772949 + Missense_Mutation SNP C C G novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 71772949 71772949 PHKA1 23 C C G 32 ARMCX1 51309 broad.mit.edu 36 X 100694665 100694665 + Silent SNP C C T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 100694665 100694665 ARMCX1 23 C C T 19 LRCH2 57631 broad.mit.edu 36 X 114311156 114311156 + Silent SNP T T C novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 114311156 114311156 LRCH2 23 T T C 51 GPR119 139760 broad.mit.edu 36 X 129346511 129346511 + Missense_Mutation SNP G G T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 129346511 129346511 GPR119 23 G G T 46 SLC9A6 10479 broad.mit.edu 36 X 134920373 134920373 + Missense_Mutation SNP G G T novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 134920373 134920373 SLC9A6 23 G G T 46 TTLL7 79739 broad.mit.edu 36 1 84180810 84180810 + Frame_Shift_Del DEL A - A novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 84180810 84180810 TTLL7 1 A - A 15 MADD 8567 broad.mit.edu 36 11 47254216 47254219 + Frame_Shift_Del DEL CTTC - CTTC novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 47254216 47254219 MADD 11 CTTC - CTTC 32 PRPF39 55015 broad.mit.edu 36 14 44653189 44653191 + In_Frame_Del DEL TAA - TAA novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 44653189 44653191 PRPF39 14 TAA - TAA 61 GPR179 440435 broad.mit.edu 36 17 33737073 33737098 + Frame_Shift_Del DEL CGGAATCTGCTGGGGCAGTGGTCTCC - - novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 33737073 33737098 GPR179 17 CGGAATCTGCTGGGGCAGTGGTCTCC - - 19 TGM3 7053 broad.mit.edu 36 20 2268586 2268605 + Frame_Shift_Del DEL GCTGATGGTGGAGGGAAGCG - GCTGATGGTGGAGGGAAGCG novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 2268586 2268605 TGM3 20 GCTGATGGTGGAGGGAAGCG - GCTGATGGTGGAGGGAAGCG 46 RFTN1 23180 broad.mit.edu 36 3 16333370 16333373 + Frame_Shift_Del DEL ACTT - - novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 16333370 16333373 RFTN1 3 ACTT - - 10 KIAA1109 84162 broad.mit.edu 36 4 123487367 123487385 + Splice_Site_Del DEL TAAGCTTGTTATGTAATTT - TAAGCTTGTTATGTAATTT novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Splice_Site_Del DEL 123487367 123487385 KIAA1109 4 TAAGCTTGTTATGTAATTT - TAAGCTTGTTATGTAATTT 57 FAT4 79633 broad.mit.edu 36 4 126586986 126586991 + In_Frame_Del DEL AAAGAT - - novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 126586986 126586991 FAT4 4 AAAGAT - - 1 MSN 4478 broad.mit.edu 36 X 64875673 64875678 + In_Frame_Del DEL GGCAGA - GGCAGA novel Unknown TCGA-09-2050-01 TCGA-09-2050-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 64875673 64875678 MSN 23 GGCAGA - GGCAGA 43