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 LEPRE1 64175 broad.mit.edu 36 1 42993203 42993203 + Missense_Mutation SNP G G T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 42993203 42993203 LEPRE1 1 G G T 44 LRRC7 57554 broad.mit.edu 36 1 70274829 70274829 + Missense_Mutation SNP G G C novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 70274829 70274829 LRRC7 1 G G C 39 ASTN1 460 broad.mit.edu 36 1 175266704 175266704 + Missense_Mutation SNP G G T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 175266704 175266704 ASTN1 1 G G T 48 OBSCN 84033 broad.mit.edu 36 1 226576369 226576369 + Silent SNP C C A novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 226576369 226576369 OBSCN 1 C C A 22 HIST3H2A 92815 broad.mit.edu 36 1 226711851 226711851 + Silent SNP C C T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 226711851 226711851 HIST3H2A 1 C C T 25 RYR2 6262 broad.mit.edu 36 1 236013917 236013917 + Silent SNP C C T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 236013917 236013917 RYR2 1 C C T 31 OR2M2 391194 broad.mit.edu 36 1 246409927 246409927 + Missense_Mutation SNP A A G novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 246409927 246409927 OR2M2 1 A A G 7 C10orf113 387638 broad.mit.edu 36 10 21475310 21475310 + Missense_Mutation SNP C C G novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 21475310 21475310 C10orf113 10 C C G 17 ARID5B 84159 broad.mit.edu 36 10 63520721 63520721 + Missense_Mutation SNP A A T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 63520721 63520721 ARID5B 10 A A T 9 NLRP14 338323 broad.mit.edu 36 11 7027589 7027589 + Silent SNP A A T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 7027589 7027589 NLRP14 11 A A T 11 FNBP4 23360 broad.mit.edu 36 11 47712212 47712212 + Missense_Mutation SNP A A C novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 47712212 47712212 FNBP4 11 A A C 2 BARX2 8538 broad.mit.edu 36 11 128812028 128812028 + Missense_Mutation SNP G G T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 128812028 128812028 BARX2 11 G G T 36 COPS7A 50813 broad.mit.edu 36 12 6708813 6708813 + Missense_Mutation SNP A A G novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 6708813 6708813 COPS7A 12 A A G 14 CD163 9332 broad.mit.edu 36 12 7531354 7531354 + Missense_Mutation SNP T T C novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 T C T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 7531354 7531354 CD163 12 T T C 64 DDX47 51202 broad.mit.edu 36 12 12865868 12865868 + Missense_Mutation SNP G G T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 12865868 12865868 DDX47 12 G G T 44 C12orf40 283461 broad.mit.edu 36 12 38363090 38363090 + Missense_Mutation SNP G G T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 38363090 38363090 C12orf40 12 G G T 36 C12orf40 283461 broad.mit.edu 36 12 38401072 38401072 + Missense_Mutation SNP T T G novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 38401072 38401072 C12orf40 12 T T G 59 KRT79 338785 broad.mit.edu 36 12 51513997 51513997 + Missense_Mutation SNP A A T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 51513997 51513997 KRT79 12 A A T 5 LRRIQ1 84125 broad.mit.edu 36 12 84024434 84024434 + Missense_Mutation SNP T T C novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 84024434 84024434 LRRIQ1 12 T T C 56 RPH3A 22895 broad.mit.edu 36 12 111770015 111770015 + Missense_Mutation SNP A A T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 111770015 111770015 RPH3A 12 A A T 11 CIT 11113 broad.mit.edu 36 12 118635783 118635783 + Missense_Mutation SNP C C T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 118635783 118635783 CIT 12 C C T 23 DIABLO 56616 broad.mit.edu 36 12 121259056 121259056 + Missense_Mutation SNP G G T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 121259056 121259056 DIABLO 12 G G T 44 PABPC3 5042 broad.mit.edu 36 13 24569197 24569197 + Missense_Mutation SNP G G C novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 24569197 24569197 PABPC3 13 G G C 41 GPR12 2835 broad.mit.edu 36 13 26231719 26231719 + Silent SNP T T C novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 T C T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 26231719 26231719 GPR12 13 T T C 61 ESD 2098 broad.mit.edu 36 13 46259170 46259170 + Silent SNP C C A novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 46259170 46259170 ESD 13 C C A 17 KLF5 688 broad.mit.edu 36 13 72534581 72534581 + Missense_Mutation SNP G G T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 G T G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 72534581 72534581 KLF5 13 G G T 46 TEP1 7011 broad.mit.edu 36 14 19921788 19921788 + Missense_Mutation SNP G G T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 19921788 19921788 TEP1 14 G G T 33 PNN 5411 broad.mit.edu 36 14 38719972 38719972 + Missense_Mutation SNP T T A novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 38719972 38719972 PNN 14 T T A 49 NAA30 122830 broad.mit.edu 36 14 56927998 56927998 + Silent SNP C C A novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 56927998 56927998 NAA30 14 C C A 22 KIAA0586 9786 broad.mit.edu 36 14 58008728 58008728 + Missense_Mutation SNP A A G novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 A G A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 58008728 58008728 KIAA0586 14 A A G 12 GPR176 11245 broad.mit.edu 36 15 37880903 37880903 + Missense_Mutation SNP G G T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 37880903 37880903 GPR176 15 G G T 44 TYRO3 7301 broad.mit.edu 36 15 39646884 39646884 + Missense_Mutation SNP C C G novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 39646884 39646884 TYRO3 15 C C G 28 EPB42 2038 broad.mit.edu 36 15 41286022 41286022 + Silent SNP G G C novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 41286022 41286022 EPB42 15 G G C 47 SPG11 80208 broad.mit.edu 36 15 42740010 42740010 + Silent SNP A A G novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 42740010 42740010 SPG11 15 A A G 13 SLC28A2 9153 broad.mit.edu 36 15 43345143 43345143 + Missense_Mutation SNP T T C novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 43345143 43345143 SLC28A2 15 T T C 57 AQP9 366 broad.mit.edu 36 15 56252647 56252647 + Missense_Mutation SNP G G C novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 56252647 56252647 AQP9 15 G G C 36 CLDN6 9074 broad.mit.edu 36 16 3005621 3005621 + Missense_Mutation SNP G G C novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 3005621 3005621 CLDN6 16 G G C 43 ADCY9 115 broad.mit.edu 36 16 3956250 3956250 + Missense_Mutation SNP T T C novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 T C T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 3956250 3956250 ADCY9 16 T T C 50 ZC3H7A 29066 broad.mit.edu 36 16 11768901 11768901 + Missense_Mutation SNP G G C novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 11768901 11768901 ZC3H7A 16 G G C 48 GDE1 51573 broad.mit.edu 36 16 19435914 19435914 + Silent SNP A A T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 19435914 19435914 GDE1 16 A A T 7 DNAH3 55567 broad.mit.edu 36 16 20938586 20938586 + Missense_Mutation SNP C C G novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 20938586 20938586 DNAH3 16 C C G 30 CNOT1 23019 broad.mit.edu 36 16 57136774 57136774 + Missense_Mutation SNP T T G novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 57136774 57136774 CNOT1 16 T T G 62 DLG4 1742 broad.mit.edu 36 17 7037754 7037754 + Missense_Mutation SNP C C T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 7037754 7037754 DLG4 17 C C T 31 TEKT3 64518 broad.mit.edu 36 17 15175140 15175140 + Missense_Mutation SNP T T A novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 15175140 15175140 TEKT3 17 T T A 54 C17orf39 79018 broad.mit.edu 36 17 17902990 17902990 + Silent SNP C C T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 17902990 17902990 C17orf39 17 C C T 19 RHOT1 55288 broad.mit.edu 36 17 27553952 27553952 + Missense_Mutation SNP G G C novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 27553952 27553952 RHOT1 17 G G C 48 GGNBP2 79893 broad.mit.edu 36 17 32017633 32017633 + Missense_Mutation SNP G G C novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 32017633 32017633 GGNBP2 17 G G C 33 CCR10 2826 broad.mit.edu 36 17 38086132 38086132 + Silent SNP T T C novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 38086132 38086132 CCR10 17 T T C 56 KIF2B 84643 broad.mit.edu 36 17 49256683 49256683 + Missense_Mutation SNP G G C novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 49256683 49256683 KIF2B 17 G G C 33 RNF213 57674 broad.mit.edu 36 17 75934213 75934213 + Missense_Mutation SNP A A C novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 75934213 75934213 RNF213 17 A A C 16 CEP192 55125 broad.mit.edu 36 18 13104130 13104130 + Missense_Mutation SNP G G C novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 13104130 13104130 CEP192 18 G G C 34 DSG3 1830 broad.mit.edu 36 18 27300615 27300615 + Silent SNP C C T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 27300615 27300615 DSG3 18 C C T 23 RFX2 5990 broad.mit.edu 36 19 5953737 5953737 + Missense_Mutation SNP C C G novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 5953737 5953737 RFX2 19 C C G 19 CTXN1 404217 broad.mit.edu 36 19 7896283 7896283 + Silent SNP C C G novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 7896283 7896283 CTXN1 19 C C G 25 MUC16 94025 broad.mit.edu 36 19 8935946 8935946 + Missense_Mutation SNP G G C novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 8935946 8935946 MUC16 19 G G C 34 PRKCSH 5589 broad.mit.edu 36 19 11408013 11408013 + Silent SNP C C T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 11408013 11408013 PRKCSH 19 C C T 29 PGLYRP2 114770 broad.mit.edu 36 19 15440505 15440505 + Missense_Mutation SNP G G T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 15440505 15440505 PGLYRP2 19 G G T 47 C19orf55 148137 broad.mit.edu 36 19 40947603 40947603 + Silent SNP C C T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 40947603 40947603 C19orf55 19 C C T 17 HKR1 284459 broad.mit.edu 36 19 42544976 42544976 + Missense_Mutation SNP C C T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 42544976 42544976 HKR1 19 C C T 30 CATSPERG 57828 broad.mit.edu 36 19 43553175 43553175 + Missense_Mutation SNP C C T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 43553175 43553175 CATSPERG 19 C C T 32 CALM3 808 broad.mit.edu 36 19 51804235 51804235 + Missense_Mutation SNP G G C novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 51804235 51804235 CALM3 19 G G C 45 LOC391343 391343 broad.mit.edu 36 2 895896 895896 + Missense_Mutation SNP T T A novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 895896 895896 LOC391343 2 T T A 59 BIRC6 57448 broad.mit.edu 36 2 32543691 32543691 + Missense_Mutation SNP C C G novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 32543691 32543691 BIRC6 2 C C G 29 PUS10 150962 broad.mit.edu 36 2 61033722 61033722 + Nonsense_Mutation SNP C C A novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 61033722 61033722 PUS10 2 C C A 32 ADD2 119 broad.mit.edu 36 2 70753936 70753936 + Missense_Mutation SNP C C G novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 70753936 70753936 ADD2 2 C C G 18 CNTNAP5 129684 broad.mit.edu 36 2 125246891 125246891 + Missense_Mutation SNP T T C novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 125246891 125246891 CNTNAP5 2 T T C 59 MYO7B 4648 broad.mit.edu 36 2 128101356 128101356 + Splice_Site_SNP SNP G G T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 128101356 128101356 MYO7B 2 G G T 44 MFSD6 54842 broad.mit.edu 36 2 191009653 191009653 + Missense_Mutation SNP C C G novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 191009653 191009653 MFSD6 2 C C G 21 CHPF 79586 broad.mit.edu 36 2 220113991 220113992 + Missense_Mutation DNP GG GG AT novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 220113991 220113992 CHPF 2 GG GG AT 35 PTMA 5757 broad.mit.edu 36 2 232281666 232281666 + Silent SNP A A G novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 232281666 232281666 PTMA 2 A A G 7 INPP5D 3635 broad.mit.edu 36 2 233695067 233695067 + Missense_Mutation SNP G G A novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 233695067 233695067 INPP5D 2 G G A 37 UGT1A1 54658 broad.mit.edu 36 2 234334195 234334195 + Silent SNP C C T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 234334195 234334195 UGT1A1 2 C C T 20 FARP2 9855 broad.mit.edu 36 2 242044963 242044964 + Silent DNP AG AG TC novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Silent DNP 242044963 242044964 FARP2 2 AG AG TC 7 DPM1 8813 broad.mit.edu 36 20 49008446 49008446 + Missense_Mutation SNP G G T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 49008446 49008446 DPM1 20 G G T 37 CTCFL 140690 broad.mit.edu 36 20 55511966 55511966 + Missense_Mutation SNP A A G novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 55511966 55511966 CTCFL 20 A A G 12 OSBP2 23762 broad.mit.edu 36 22 29421221 29421221 + Missense_Mutation SNP G G C novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 29421221 29421221 OSBP2 22 G G C 33 TMPRSS6 164656 broad.mit.edu 36 22 35796501 35796501 + Missense_Mutation SNP T T G novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 35796501 35796501 TMPRSS6 22 T T G 50 SAMM50 25813 broad.mit.edu 36 22 42703319 42703319 + Missense_Mutation SNP G G A novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 42703319 42703319 SAMM50 22 G G A 33 LHFPL4 375323 broad.mit.edu 36 3 9522805 9522805 + Silent SNP C C T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 9522805 9522805 LHFPL4 3 C C T 23 ATP2B2 491 broad.mit.edu 36 3 10466053 10466053 + Missense_Mutation SNP G G A novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 10466053 10466053 ATP2B2 3 G G A 38 AZI2 64343 broad.mit.edu 36 3 28355078 28355078 + Silent SNP G G A novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 28355078 28355078 AZI2 3 G G A 39 NPHP3 27031 broad.mit.edu 36 3 133916620 133916620 + Missense_Mutation SNP T T A novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 133916620 133916620 NPHP3 3 T T A 56 TSC22D2 9819 broad.mit.edu 36 3 151610420 151610420 + Missense_Mutation SNP C C G novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 151610420 151610420 TSC22D2 3 C C G 30 MUC4 4585 broad.mit.edu 36 3 197000647 197000647 + Silent SNP G G C novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 197000647 197000647 MUC4 3 G G C 47 UGT2B10 7365 broad.mit.edu 36 4 69716716 69716716 + Silent SNP T T C novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 T C T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 69716716 69716716 UGT2B10 4 T T C 64 PPP3CA 5530 broad.mit.edu 36 4 102223386 102223386 + Silent SNP G G C novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 102223386 102223386 PPP3CA 4 G G C 43 PCDHGA12 26025 broad.mit.edu 36 5 140792798 140792798 + Missense_Mutation SNP C C T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 140792798 140792798 PCDHGA12 5 C C T 31 HIST1H3J 8356 broad.mit.edu 36 6 27966523 27966523 + Silent SNP G G C novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 27966523 27966523 HIST1H3J 6 G G C 46 RPP21 79897 broad.mit.edu 36 6 30422273 30422273 + Silent SNP C C A novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 30422273 30422273 RPP21 6 C C A 32 XPO5 57510 broad.mit.edu 36 6 43600256 43600256 + Silent SNP G G A novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 43600256 43600256 XPO5 6 G G A 35 EYS 346007 broad.mit.edu 36 6 66171839 66171839 + Missense_Mutation SNP C C G novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 66171839 66171839 EYS 6 C C G 20 IMPG1 3617 broad.mit.edu 36 6 76717379 76717379 + Missense_Mutation SNP G G A novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 76717379 76717379 IMPG1 6 G G A 43 ELOVL4 6785 broad.mit.edu 36 6 80688095 80688095 + Missense_Mutation SNP C C A novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 80688095 80688095 ELOVL4 6 C C A 18 HTR1E 3354 broad.mit.edu 36 6 87782042 87782042 + Missense_Mutation SNP G G C novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 87782042 87782042 HTR1E 6 G G C 47 TIAM2 26230 broad.mit.edu 36 6 155500014 155500014 + Silent SNP C C A novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 155500014 155500014 TIAM2 6 C C A 21 CPVL 54504 broad.mit.edu 36 7 29036851 29036851 + Missense_Mutation SNP G G C novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 29036851 29036851 CPVL 7 G G C 48 UPP1 7378 broad.mit.edu 36 7 48114399 48114399 + Missense_Mutation SNP C C T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 48114399 48114399 UPP1 7 C C T 31 KIAA1324L 222223 broad.mit.edu 36 7 86379340 86379340 + Missense_Mutation SNP C C T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 86379340 86379340 KIAA1324L 7 C C T 20 CTTNBP2 83992 broad.mit.edu 36 7 117173346 117173346 + Missense_Mutation SNP C C G novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 117173346 117173346 CTTNBP2 7 C C G 28 IQUB 154865 broad.mit.edu 36 7 122939369 122939369 + Missense_Mutation SNP C C A novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 122939369 122939369 IQUB 7 C C A 20 TTC26 79989 broad.mit.edu 36 7 138482481 138482481 + Silent SNP C C T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 138482481 138482481 TTC26 7 C C T 29 DUSP4 1846 broad.mit.edu 36 8 29258942 29258942 + Silent SNP G G A novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 29258942 29258942 DUSP4 8 G G A 40 ZFPM2 23414 broad.mit.edu 36 8 106882755 106882755 + Missense_Mutation SNP C C G novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 C G C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 106882755 106882755 ZFPM2 8 C C G 26 SLA 6503 broad.mit.edu 36 8 134141616 134141616 + Missense_Mutation SNP G G A novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 134141616 134141616 SLA 8 G G A 45 CNTFR 1271 broad.mit.edu 36 9 34554662 34554662 + Missense_Mutation SNP C C G novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 34554662 34554662 CNTFR 9 C C G 26 TLN1 7094 broad.mit.edu 36 9 35689450 35689450 + Missense_Mutation SNP C C A novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 35689450 35689450 TLN1 9 C C A 32 SMC5 23137 broad.mit.edu 36 9 72128856 72128856 + Missense_Mutation SNP T T C novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 72128856 72128856 SMC5 9 T T C 50 RGS3 5998 broad.mit.edu 36 9 115264277 115264277 + Silent SNP C C T novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 115264277 115264277 RGS3 9 C C T 29 FAM48B2 170067 broad.mit.edu 36 X 24239593 24239593 + Silent SNP A A C novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 24239593 24239593 FAM48B2 23 A A C 1 ZCCHC5 203430 broad.mit.edu 36 X 77799795 77799795 + Missense_Mutation SNP C C G novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 77799795 77799795 ZCCHC5 23 C C G 20 RPL10 6134 broad.mit.edu 36 X 153282294 153282294 + Missense_Mutation SNP A A C novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 153282294 153282294 RPL10 23 A A C 8 TP53 7157 broad.mit.edu 36 17 7518239 7518247 + In_Frame_Del DEL GTGATGATG GTGATGATG - novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 7518239 7518247 TP53 17 GTGATGATG GTGATGATG - 48 PSAT1 29968 broad.mit.edu 36 9 80132916 80132922 + Frame_Shift_Del DEL AGGGCAT - AGGGCAT novel Unknown TCGA-23-1031-01 TCGA-23-1031-10 - AGGGCAT AGGGCAT AGGGCAT Unknown Valid Somatic Phase_I Capture Illumina GAIIx Broad Frame_Shift_Del DEL 80132916 80132922 PSAT1 9 AGGGCAT - AGGGCAT 3