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 CSMD2 114784 broad.mit.edu 36 1 33843510 33843510 + Missense_Mutation SNP C C A novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 33843510 33843510 CSMD2 1 C C A 26 MACF1 23499 broad.mit.edu 36 1 39626601 39626601 + Missense_Mutation SNP A A G novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 39626601 39626601 MACF1 1 A A G 2 IPO13 9670 broad.mit.edu 36 1 44196337 44196337 + Missense_Mutation SNP G G A novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 44196337 44196337 IPO13 1 G G A 48 SRSF11 9295 broad.mit.edu 36 1 70488228 70488228 + Missense_Mutation SNP G G C novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 70488228 70488228 SRSF11 1 G G C 33 KPRP 448834 broad.mit.edu 36 1 151000175 151000175 + Missense_Mutation SNP G G A novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 151000175 151000175 KPRP 1 G G A 38 USH2A 7399 broad.mit.edu 36 1 213915145 213915145 + Missense_Mutation SNP T T C novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 213915145 213915145 USH2A 1 T T C 52 OR2T5 401993 broad.mit.edu 36 1 246718654 246718654 + Missense_Mutation SNP G G C novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 246718654 246718654 OR2T5 1 G G C 48 GAD2 2572 broad.mit.edu 36 10 26602626 26602626 + Missense_Mutation SNP G G T novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 26602626 26602626 GAD2 10 G G T 42 ADAMTS14 140766 broad.mit.edu 36 10 72138484 72138484 + Missense_Mutation SNP G G C novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 72138484 72138484 ADAMTS14 10 G G C 44 ZNF215 7762 broad.mit.edu 36 11 6920968 6920968 + Missense_Mutation SNP C C G novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 6920968 6920968 ZNF215 11 C C G 24 SBF2 81846 broad.mit.edu 36 11 9767406 9767406 + Silent SNP C C T novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 9767406 9767406 SBF2 11 C C T 32 METT5D1 196074 broad.mit.edu 36 11 28091635 28091635 + Missense_Mutation SNP T T G novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 28091635 28091635 METT5D1 11 T T G 50 TMEM109 79073 broad.mit.edu 36 11 60443814 60443814 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 60443814 60443814 TMEM109 11 C C T 24 CHD4 1108 broad.mit.edu 36 12 6571219 6571219 + Missense_Mutation SNP C C A novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 6571219 6571219 CHD4 12 C C A 21 ESYT1 23344 broad.mit.edu 36 12 54817331 54817331 + Missense_Mutation SNP G G C novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 54817331 54817331 ESYT1 12 G G C 43 NACA 4666 broad.mit.edu 36 12 55394411 55394411 + Splice_Site_SNP SNP A A T novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 55394411 55394411 NACA 12 A A T 14 C12orf29 91298 broad.mit.edu 36 12 86963564 86963564 + Missense_Mutation SNP G G A novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 86963564 86963564 C12orf29 12 G G A 46 EXOC5 10640 broad.mit.edu 36 14 56768034 56768034 + Missense_Mutation SNP A A T novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 56768034 56768034 EXOC5 14 A A T 12 CCDC88C 440193 broad.mit.edu 36 14 90815397 90815397 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 90815397 90815397 CCDC88C 14 C C T 23 AHNAK2 113146 broad.mit.edu 36 14 104487289 104487289 + Silent SNP C C G novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 104487289 104487289 AHNAK2 14 C C G 17 RYR3 6263 broad.mit.edu 36 15 31646215 31646215 + Silent SNP G G A novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 31646215 31646215 RYR3 15 G G A 46 CSK 1445 broad.mit.edu 36 15 72881724 72881724 + Splice_Site_SNP SNP G G T novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 72881724 72881724 CSK 15 G G T 34 MGRN1 23295 broad.mit.edu 36 16 4640457 4640457 + Missense_Mutation SNP T T G novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 4640457 4640457 MGRN1 16 T T G 55 MYH11 4629 broad.mit.edu 36 16 15751638 15751638 + Missense_Mutation SNP A A C novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 15751638 15751638 MYH11 16 A A C 7 GOSR1 9527 broad.mit.edu 36 17 25871136 25871136 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 25871136 25871136 GOSR1 17 C C T 29 uc002igz.2 284071 broad.mit.edu 36 17 40100965 40100965 + Silent SNP T T C novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 40100965 40100965 uc002igz.2 17 T T C 56 MARCH2 51257 broad.mit.edu 36 19 8409305 8409305 + Nonsense_Mutation SNP G G T novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 8409305 8409305 MARCH2 19 G G T 37 ZNF20 7568 broad.mit.edu 36 19 12105390 12105390 + Missense_Mutation SNP C C G novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 12105390 12105390 ZNF20 19 C C G 17 ZNF708 7562 broad.mit.edu 36 19 21283944 21283944 + Missense_Mutation SNP T T C novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 21283944 21283944 ZNF708 19 T T C 54 GSK3A 2931 broad.mit.edu 36 19 47428573 47428573 + Missense_Mutation SNP G G C novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 47428573 47428573 GSK3A 19 G G C 48 ZNF45 7596 broad.mit.edu 36 19 49110073 49110073 + Missense_Mutation SNP C C G novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 49110073 49110073 ZNF45 19 C C G 26 BIRC6 57448 broad.mit.edu 36 2 32541905 32541905 + Silent SNP A A C novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 32541905 32541905 BIRC6 2 A A C 14 LTBP1 4052 broad.mit.edu 36 2 33353618 33353618 + Silent SNP C C T novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 33353618 33353618 LTBP1 2 C C T 26 LRRTM4 80059 broad.mit.edu 36 2 77599824 77599824 + Missense_Mutation SNP G G C novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 77599824 77599824 LRRTM4 2 G G C 40 ST6GAL2 84620 broad.mit.edu 36 2 106789823 106789823 + Missense_Mutation SNP T T C novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 106789823 106789823 ST6GAL2 2 T T C 50 HSPA12B 116835 broad.mit.edu 36 20 3673632 3673632 + Missense_Mutation SNP G G T novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 3673632 3673632 HSPA12B 20 G G T 34 ITSN1 6453 broad.mit.edu 36 21 34130729 34130729 + Missense_Mutation SNP G G C novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 34130729 34130729 ITSN1 21 G G C 41 PFKL 5211 broad.mit.edu 36 21 44571033 44571033 + Missense_Mutation SNP A A G novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 44571033 44571033 PFKL 21 A A G 8 TCF20 6942 broad.mit.edu 36 22 40940142 40940142 + Missense_Mutation SNP G G T novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 40940142 40940142 TCF20 22 G G T 41 WNT7B 7477 broad.mit.edu 36 22 44705751 44705751 + Missense_Mutation SNP G G C novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 44705751 44705751 WNT7B 22 G G C 42 KALRN 8997 broad.mit.edu 36 3 125615117 125615117 + Silent SNP G G C novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 125615117 125615117 KALRN 3 G G C 41 PIK3R4 30849 broad.mit.edu 36 3 131925103 131925103 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 131925103 131925103 PIK3R4 3 C C T 26 EPHB1 2047 broad.mit.edu 36 3 136153129 136153129 + Missense_Mutation SNP C C A novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 136153129 136153129 EPHB1 3 C C A 20 CCDC39 339829 broad.mit.edu 36 3 181861186 181861186 + Missense_Mutation SNP T T C novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 181861186 181861186 CCDC39 3 T T C 64 KLHL24 54800 broad.mit.edu 36 3 184879744 184879744 + Nonsense_Mutation SNP C C G novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 184879744 184879744 KLHL24 3 C C G 17 GPRIN3 285513 broad.mit.edu 36 4 90389357 90389357 + Missense_Mutation SNP T T G novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 90389357 90389357 GPRIN3 4 T T G 63 FAT1 2195 broad.mit.edu 36 4 187786453 187786453 + Missense_Mutation SNP G G C novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 187786453 187786453 FAT1 4 G G C 38 ANKRD55 79722 broad.mit.edu 36 5 55434103 55434103 + Missense_Mutation SNP G G T novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 55434103 55434103 ANKRD55 5 G G T 44 PDLIM7 9260 broad.mit.edu 36 5 176843490 176843490 + Missense_Mutation SNP G G C novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 176843490 176843490 PDLIM7 5 G G C 44 BACH2 60468 broad.mit.edu 36 6 90716963 90716963 + Missense_Mutation SNP T T G novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 90716963 90716963 BACH2 6 T T G 57 MAP3K7 6885 broad.mit.edu 36 6 91335017 91335017 + Missense_Mutation SNP T T C novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 91335017 91335017 MAP3K7 6 T T C 49 HIVEP2 3097 broad.mit.edu 36 6 143135840 143135840 + Missense_Mutation SNP A A G novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 143135840 143135840 HIVEP2 6 A A G 4 SAMD9 54809 broad.mit.edu 36 7 92571071 92571071 + Missense_Mutation SNP C C G novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 92571071 92571071 SAMD9 7 C C G 32 PPP1R3A 5506 broad.mit.edu 36 7 113307084 113307084 + Silent SNP G G C novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 113307084 113307084 PPP1R3A 7 G G C 46 POT1 25913 broad.mit.edu 36 7 124298223 124298223 + Missense_Mutation SNP A A G novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 124298223 124298223 POT1 7 A A G 4 C7orf29 113763 broad.mit.edu 36 7 149659030 149659030 + Missense_Mutation SNP G G C novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 149659030 149659030 C7orf29 7 G G C 41 NEFM 4741 broad.mit.edu 36 8 24829055 24829055 + Silent SNP G G A novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 24829055 24829055 NEFM 8 G G A 43 PIGO 84720 broad.mit.edu 36 9 35081650 35081650 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 35081650 35081650 PIGO 9 C C T 23 ABCA1 19 broad.mit.edu 36 9 106631078 106631078 + Nonsense_Mutation SNP C C T novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 106631078 106631078 ABCA1 9 C C T 18 SPIN2A 54466 broad.mit.edu 36 X 57179003 57179003 + Silent SNP G G A novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 57179003 57179003 SPIN2A 23 G G A 33 AWAT2 158835 broad.mit.edu 36 X 69178893 69178893 + Missense_Mutation SNP C C A novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 69178893 69178893 AWAT2 23 C C A 18 KPNA3 3839 broad.mit.edu 36 13 49181737 49181741 + Frame_Shift_Del DEL AAGAG - - novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 49181737 49181741 KPNA3 13 AAGAG - - 13 ALOX12 239 broad.mit.edu 36 17 6854133 6854142 + Frame_Shift_Del DEL CATCTCATGG - CATCTCATGG novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 6854133 6854142 ALOX12 17 CATCTCATGG - CATCTCATGG 21 TP53 7157 broad.mit.edu 36 17 7517744 7517745 + Frame_Shift_Del DEL CT - CT novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 7517744 7517745 TP53 17 CT - CT 24 ZNF708 7562 broad.mit.edu 36 19 21268402 21268402 + Frame_Shift_Del DEL G - G novel Unknown TCGA-61-2109-01 TCGA-61-2109-11 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 21268402 21268402 ZNF708 19 G - G 47