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 Transcript_Id Exon ChromChange AAChange Genome_Plus_Minus_10_Bp Drug_Target TTotCov TVarCov NTotCov NVarCov dbSNPPopFreq COSMIC_Gene_Freq COSMIC_Site_Freq TVarRat NVarRat dbSNP_Strength dbSNP_AF dbSNP_PopFreq Confidence Algorithm AGRN 375790 hgsc.bcm.edu hg19 1 984390 984390 + Missense_Mutation SNP G G T novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . AGRN NM_198576 exon24 c.G4249T p.G1417C GCCCGGGGCAAGG . 100.0 27.0 194.0 0.0 . 110 . . . none . . PASS Atlas-SNP KIF1B 23095 hgsc.bcm.edu hg19 1 10394605 10394605 + Silent SNP G G A novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . KIF1B NM_015074 exon26 c.G2814A p.L938L TCTGCTGTATCCC . 81.0 33.0 90.0 0.0 . 242 . . . none . . PASS Atlas-SNP PEX14 5195 hgsc.bcm.edu hg19 1 10596271 10596271 + Missense_Mutation SNP T T G novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . PEX14 NM_004565 exon3 c.T86G p.I29S ACCAGATTGCCAC . 226.0 87.0 336.0 1.0 . 40 . . . none . . PASS Atlas-SNP GJA4 2701 hgsc.bcm.edu hg19 1 35260710 35260710 + Missense_Mutation SNP G G C novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . GJA4 NM_002060 exon2 c.G896C p.R299T AGGAGAGGCTGGC . 40.0 15.0 47.0 0.0 . 25 . . . none . . PASS Atlas-SNP SLFNL1 200172 hgsc.bcm.edu hg19 1 41486067 41486067 + Missense_Mutation SNP G G T rs189387361 bycluster;by1000genomes;alternate_allele TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . SLFNL1 NM_001168247 exon3 c.C266A p.P89Q TTCCGCGGCCGCC . 33.0 9.0 50.0 0.0 . 37 . . . alt G|0.999;A|0.001 . PASS Atlas-SNP SZT2 23334 hgsc.bcm.edu hg19 1 43896443 43896443 + Missense_Mutation SNP G G C novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . SZT2 NM_015284 exon31 c.G4586C p.S1529T TGTGCAGCCTGCC . 39.0 14.0 29.0 0.0 . 383 . . . none . . PASS Atlas-SNP ZCCHC11 23318 hgsc.bcm.edu hg19 1 52941009 52941009 + Missense_Mutation SNP A A C novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . ZCCHC11 NM_001009881 exon13 c.T2222G p.M741R GTTGCCATATTGT . 63.0 10.0 90.0 0.0 . 151 . . . none . . PASS Atlas-SNP ARHGAP29 9411 hgsc.bcm.edu hg19 1 94650461 94650461 + Silent SNP G G T novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . ARHGAP29 NM_004815 exon18 c.C2076A p.A692A CTCTGAGGCACAT . 90.0 11.0 69.0 0.0 . 132 . . . none . . PASS Atlas-SNP SASS6 163786 hgsc.bcm.edu hg19 1 100573433 100573433 + Missense_Mutation SNP T T A novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . SASS6 NM_194292 exon9 c.A989T p.E330V TTGATTTCCTGTT . 64.0 23.0 84.0 0.0 . 61 . . . none . . PASS Atlas-SNP IGSF9 57549 hgsc.bcm.edu hg19 1 159912854 159912854 + Missense_Mutation SNP C C T novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . IGSF9 NM_001135050 exon3 c.G146A p.R49Q GGGGGCCGGCCGG . 188.0 12.0 200.0 0.0 . 123 . . . none . . PASS Atlas-SNP SLC9C2 284525 hgsc.bcm.edu hg19 1 173503688 173503688 + Missense_Mutation SNP C C T novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . . NM_178527 exon16 c.G1909A p.V637I CTGATACATTTAA . 457.0 218.0 320.0 1.0 . . . . . none . . PASS Atlas-SNP KIAA1614 57710 hgsc.bcm.edu hg19 1 180882414 180882414 + Missense_Mutation SNP C C T novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . KIAA1614 NM_020950 exon1 c.C35T p.A12V AACCCGCGGGCGG . 181.0 50.0 236.0 0.0 . 75 . . . none . . PASS Atlas-SNP NFASC 23114 hgsc.bcm.edu hg19 1 204955212 204955212 + Missense_Mutation SNP G G A novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . NFASC NM_001160331 exon21 c.G2794A p.E932K CGCAGTGAGACCA . 108.0 15.0 136.0 0.0 . 396 . . . none . . PASS Atlas-SNP LCLAT1 253558 hgsc.bcm.edu hg19 2 30863435 30863435 + Missense_Mutation SNP T T A novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . LCLAT1 NM_182551 exon7 c.T1195A p.Y399N GCATGTTACCGAC . 97.0 10.0 92.0 0.0 . 51 . . . none . . PASS Atlas-SNP TMEM17 200728 hgsc.bcm.edu hg19 2 62729639 62729639 + Missense_Mutation SNP A A G novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . TMEM17 NM_198276 exon3 c.T251C p.I84T AGGATGATAACAG . 137.0 9.0 162.0 0.0 . 19 . . . none . . PASS Atlas-SNP KDM3A 55818 hgsc.bcm.edu hg19 2 86669203 86669203 + Silent SNP A A G novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . KDM3A NM_001146688 exon2 c.A33G p.V11V GCCGGTATTGGTG . 51.0 10.0 71.0 0.0 . 179 . . . none . . PASS Atlas-SNP CNTNAP5 129684 hgsc.bcm.edu hg19 2 125405359 125405359 + Missense_Mutation SNP A A T novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . CNTNAP5 NM_130773 exon13 c.A1898T p.Q633L CAGTGCAGCACAA . 187.0 14.0 196.0 0.0 . 405 . . . none . . PASS Atlas-SNP MAP3K19 80122 hgsc.bcm.edu hg19 2 135738784 135738784 + Missense_Mutation SNP T T C novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . . NM_025052 exon9 c.A3527G p.Y1176C TGGAGATAAGCAA . 70.0 26.0 55.0 0.0 . . . . . none . . PASS Atlas-SNP TTN 7273 hgsc.bcm.edu hg19 2 179396967 179396967 + Missense_Mutation SNP A A C novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . TTN NM_001267550 exon358 c.T104375G p.F34792C GACATGAAGTCAA . 32.0 9.0 31.0 0.0 . 18412 . . . none . . PASS Atlas-SNP XRCC5 7520 hgsc.bcm.edu hg19 2 216982471 216982471 + Missense_Mutation SNP C C A novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . XRCC5 NM_021141 exon4 c.C322A p.L108M TGAGTCCTGGATG . 71.0 20.0 55.0 0.0 . 64 . . . none . . PASS Atlas-SNP SH3BP4 23677 hgsc.bcm.edu hg19 2 235950616 235950616 + Silent SNP A A T novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . SH3BP4 NM_014521 exon4 c.A1203T p.I401I CGAGATAAAAAAT . 68.0 19.0 78.0 0.0 . 109 . . . none . . PASS Atlas-SNP DLEC1 9940 hgsc.bcm.edu hg19 3 38158502 38158502 + Missense_Mutation SNP T T C novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . DLEC1 NM_007337 exon30 c.T4216C p.S1406P TACATCTCCTTCA . 32.0 10.0 59.0 0.0 . 278 . . . none . . PASS Atlas-SNP BAP1 8314 hgsc.bcm.edu hg19 3 52443600 52443600 + Missense_Mutation SNP T T C novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 BAP1,NS,carcinoma,0,2 BAP1 NM_004656 exon3 c.A92G p.E31G TAGATCTCCTCCA . 53.0 21.0 142.0 0.0 . 371 . . . none . . PASS Atlas-SNP ITIH1 3697 hgsc.bcm.edu hg19 3 52813055 52813055 + Missense_Mutation SNP C C A novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . ITIH1 NM_002215 exon4 c.C403A p.L135I GCCGGCCTTGTCA . 24.0 6.0 54.0 0.0 . 108 . . . none . . PASS Atlas-SNP ERC2 26059 hgsc.bcm.edu hg19 3 55768866 55768866 + Missense_Mutation SNP T T C novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . ERC2 NM_015576 exon14 c.A2639G p.K880R TGCGTCTTTTTCT . 46.0 4.0 49.0 0.0 . 221 . . . none . . PASS Atlas-SNP WDR52 55779 hgsc.bcm.edu hg19 3 113125861 113125861 + Silent SNP G G A novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . WDR52 NM_001164496 exon8 c.C918T p.T306T GAGACCGGTGAAC . 150.0 28.0 101.0 0.0 . 151 . . . none . . PASS Atlas-SNP OTOL1 131149 hgsc.bcm.edu hg19 3 161220933 161220933 + Missense_Mutation SNP G G A novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . OTOL1 NM_001080440 exon4 c.G637A p.A213T CAAGGGGCTATGG . 280.0 68.0 135.0 0.0 . 63 . . . none . . PASS Atlas-SNP BCL6 604 hgsc.bcm.edu hg19 3 187446278 187446278 + Missense_Mutation SNP C C A novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . BCL6 NM_001134738 exon5 c.G1410T p.M470I GGGGTGCATGTAG . 71.0 35.0 53.0 0.0 . 107 . . . none . . PASS Atlas-SNP MUC4 4585 hgsc.bcm.edu hg19 3 195492266 195492266 + Missense_Mutation SNP C C T novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 MUC4_ENST00000463781,NS,carcinoma,0,3 MUC4 NM_018406 exon9 c.G13673A p.R4558H TCGAGACGGTAGT . 77.0 4.0 110.0 0.0 . 1505 . . . none . . PASS Atlas-SNP MUC4 4585 hgsc.bcm.edu hg19 3 195511408 195511408 + Missense_Mutation SNP C C T novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . MUC4 NM_018406 exon2 c.G7043A p.G2348D GCGTGACCTGTGG . 114.0 9.0 100.0 0.0 . 1505 . . . none . . PASS Atlas-SNP GPR98 84059 hgsc.bcm.edu hg19 5 90012405 90012405 + Nonsense_Mutation SNP C C A novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . GPR98 NM_032119 exon43 c.C9306A p.Y3102X ATTGTACATTGTT . 138.0 16.0 136.0 0.0 . 605 . . . none . . PASS Atlas-SNP MCC 4163 hgsc.bcm.edu hg19 5 112420999 112420999 + Missense_Mutation SNP C C A novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . MCC NM_001085377 exon9 c.G1407T p.E469D TTGAAGCTCTCTG . 62.0 25.0 46.0 0.0 . 234 . . . none . . PASS Atlas-SNP PCDHGB7 56099 hgsc.bcm.edu hg19 5 140797588 140797588 + Silent SNP A A C novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . PCDHGB7 NM_018927 exon1 c.A162C p.L54L GGATCTAGGGCTT . 59.0 21.0 132.0 0.0 . 117 . . . none . . PASS Atlas-SNP SH3TC2 79628 hgsc.bcm.edu hg19 5 148386485 148386485 + Missense_Mutation SNP C C G novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . SH3TC2 NM_024577 exon16 c.G3634C p.V1212L AATACACCTTGGC . 112.0 26.0 126.0 0.0 . 178 . . . none . . PASS Atlas-SNP C2 717 hgsc.bcm.edu hg19 6 31905164 31905164 + Missense_Mutation SNP C C A novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . C2 NM_000063 exon8 c.C1057A p.Q353K AACAACCAAATGC . 83.0 24.0 113.0 0.0 . 50 . . . none . . PASS Atlas-SNP AZGP1 563 hgsc.bcm.edu hg19 7 99565822 99565822 + Missense_Mutation SNP A A T novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . AZGP1 NM_001185 exon3 c.T569A p.L190Q TTCCGCAGAGTCG . 33.0 10.0 59.0 0.0 . 41 . . . none . . PASS Atlas-SNP GPR37 2861 hgsc.bcm.edu hg19 7 124387366 124387366 + Missense_Mutation SNP A A G novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . GPR37 NM_005302 exon2 c.T1055C p.L352S GCACATAAGGTGA . 58.0 6.0 43.0 0.0 . 89 . . . none . . PASS Atlas-SNP TMEM139 135932 hgsc.bcm.edu hg19 7 142983223 142983223 + Missense_Mutation SNP T T C novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . TMEM139 NM_001242773 exon3 c.T173C p.F58S TCCGGTTTCTGGA . 42.0 15.0 64.0 0.0 . 18 . . . none . . PASS Atlas-SNP PDIA4 9601 hgsc.bcm.edu hg19 7 148712027 148712027 + Missense_Mutation SNP C C A novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . PDIA4 NM_004911 exon4 c.G583T p.D195Y TGATATCTGCATC . 80.0 16.0 93.0 0.0 . 57 . . . none . . PASS Atlas-SNP TMEM176A 55365 hgsc.bcm.edu hg19 7 150500886 150500886 + Missense_Mutation SNP T T C novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . TMEM176A NM_018487 exon5 c.T521C p.L174P GAAGGCTACACCT . 58.0 25.0 66.0 0.0 . 35 . . . none . . PASS Atlas-SNP KIF13B 23303 hgsc.bcm.edu hg19 8 29024953 29024953 + Silent SNP G G T novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . KIF13B NM_015254 exon11 c.C1095A p.A365A AATTCGGGCATTA . 97.0 14.0 62.0 0.0 . 192 . . . none . . PASS Atlas-SNP KAT6A 7994 hgsc.bcm.edu hg19 8 41906305 41906305 + Nonsense_Mutation SNP G G T novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . . NM_001099412 exon3 c.C191A p.S64X TTATTTGAGACTT . 116.0 27.0 105.0 0.0 . . . . . none . . PASS Atlas-SNP ZFHX4 79776 hgsc.bcm.edu hg19 8 77776082 77776082 + Nonsense_Mutation SNP A A T novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . ZFHX4 NM_024721 exon11 c.A10132T p.K3378X AGCACAAAAGAAG . 63.0 11.0 37.0 0.0 . 878 . . . none . . PASS Atlas-SNP RIMS2 9699 hgsc.bcm.edu hg19 8 105257207 105257207 + Missense_Mutation SNP A A T novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . RIMS2 NM_001100117 exon20 c.A3398T p.E1133V CCGTGGAAATGAG . 281.0 24.0 166.0 0.0 . 1357 . . . none . . PASS Atlas-SNP C9orf72 203228 hgsc.bcm.edu hg19 9 27566893 27566893 + Missense_Mutation SNP C C T novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . C9orf72 NM_018325 exon2 c.G226A p.E76K CACTCTCTGCATT . 114.0 37.0 97.0 0.0 . 48 . . . none . . PASS Atlas-SNP TMEM2 23670 hgsc.bcm.edu hg19 9 74345097 74345097 + Missense_Mutation SNP T T C novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . TMEM2 NM_013390 exon9 c.A1846G p.T616A ACAAAGTATTCCT . 129.0 28.0 140.0 0.0 . 112 . . . none . . PASS Atlas-SNP PHF2 5253 hgsc.bcm.edu hg19 9 96421819 96421819 + Silent SNP C C T novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . PHF2 NM_005392 exon11 c.C1266T p.L422L CGAGCTCCCGGAG . 159.0 47.0 248.0 0.0 . 113 . . . none . . PASS Atlas-SNP CUBN 8029 hgsc.bcm.edu hg19 10 17110184 17110184 + Silent SNP A A G novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . CUBN NM_001081 exon21 c.T2887C p.L963L GGACTAATATATG . 138.0 52.0 100.0 0.0 . 515 . . . none . . PASS Atlas-SNP C10orf137 26098 hgsc.bcm.edu hg19 10 127411636 127411636 + Splice_Site SNP G G T novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . C10orf137 NM_001202438 exon3 c.318-1G>T . TTGGTAGCTTTGG . 93.0 6.0 107.0 0.0 . 153 . . . none . . PASS Atlas-SNP OR51Q1 390061 hgsc.bcm.edu hg19 11 5443619 5443619 + Silent SNP G G T novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . OR51Q1 NM_001004757 exon1 c.G189T p.L63L GTATCTGTTTCTC . 77.0 8.0 60.0 0.0 . 79 . . . none . . PASS Atlas-SNP NLRP10 338322 hgsc.bcm.edu hg19 11 7982378 7982378 + Missense_Mutation SNP T T G novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . NLRP10 NM_176821 exon2 c.A781C p.K261Q TCAACTTTTCTTC . 66.0 23.0 73.0 0.0 . 146 . . . none . . PASS Atlas-SNP OR4C11 219429 hgsc.bcm.edu hg19 11 55371658 55371658 + Silent SNP C C T novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . OR4C11 NM_001004700 exon1 c.G192A p.L64L AAAGGACAAATAA . 43.0 28.0 30.0 0.0 . 73 . . . none . . PASS Atlas-SNP CD5 921 hgsc.bcm.edu hg19 11 60891376 60891376 + Nonsense_Mutation SNP C C T novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . CD5 NM_014207 exon8 c.C1246T p.Q416X CAGCGCCAGTGGA . 30.0 12.0 42.0 0.0 . 52 . . . none . . PASS Atlas-SNP MED17 9440 hgsc.bcm.edu hg19 11 93535078 93535078 + Missense_Mutation SNP A A G novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . MED17 NM_004268 exon9 c.A1406G p.D469G TCAATGATGTTTA . 207.0 18.0 190.0 0.0 . 37 . . . none . . PASS Atlas-SNP KCNA5 3741 hgsc.bcm.edu hg19 12 5154784 5154784 + Missense_Mutation SNP G G T novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . KCNA5 NM_002234 exon1 c.G1471T p.V491F ATCACTGTTGGGG . 90.0 18.0 112.0 0.0 . 138 . . . none . . PASS Atlas-SNP KCNH3 23416 hgsc.bcm.edu hg19 12 49942732 49942732 + Missense_Mutation SNP G G A novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . KCNH3 NM_012284 exon8 c.G1244A p.R415Q TGGGCCGGAGGCC . 87.0 22.0 99.0 0.0 . 88 . . . none . . PASS Atlas-SNP KIAA1033 23325 hgsc.bcm.edu hg19 12 105538550 105538550 + Missense_Mutation SNP T T C novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . KIAA1033 NM_015275 exon22 c.T2234C p.L745P TAGCCCTTCATGA . 91.0 48.0 75.0 0.0 . 83 . . . none . . PASS Atlas-SNP SPATA13 221178 hgsc.bcm.edu hg19 13 24797769 24797769 + Silent SNP G G A novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . SPATA13 NM_001166271 exon2 c.G702A p.V234V CGCCGTGTGTGAG . 42.0 13.0 70.0 0.0 . 92 . . . none . . PASS Atlas-SNP RTL1 388015 hgsc.bcm.edu hg19 14 101347376 101347376 + Silent SNP G G A novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . RTL1 NM_001134888 exon1 c.C3750T p.D1250D CAGGCCGTCATGC . 79.0 9.0 116.0 0.0 . 120 . . . none . . PASS Atlas-SNP DMXL2 23312 hgsc.bcm.edu hg19 15 51799330 51799330 + Splice_Site SNP C C T novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . DMXL2 NM_015263 exon17 c.2764+1G>A . TACTTACCTAAAC . 37.0 11.0 55.0 0.0 . 262 . . . none . . PASS Atlas-SNP CNOT1 23019 hgsc.bcm.edu hg19 16 58583738 58583738 + Missense_Mutation SNP A A T novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . CNOT1 NM_206999 exon25 c.T3407A p.M1136K CTCTTCATAACCA . 106.0 27.0 66.0 0.0 . 359 . . . none . . PASS Atlas-SNP CNOT1 23019 hgsc.bcm.edu hg19 16 58615281 58615281 + Missense_Mutation SNP T T C novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . CNOT1 NM_206999 exon11 c.A1183G p.I395V TATATATGAGGTC . 123.0 46.0 115.0 0.0 . 359 . . . none . . PASS Atlas-SNP ABR 29 hgsc.bcm.edu hg19 17 1082993 1082993 + Missense_Mutation SNP G G C novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . ABR NM_021962 exon1 c.C29G p.P10R AGGCGCGGCAGGC . 169.0 38.0 226.0 0.0 . 119 . . . none . . PASS Atlas-SNP DNAH2 146754 hgsc.bcm.edu hg19 17 7689641 7689641 + Missense_Mutation SNP C C G novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . DNAH2 NM_020877 exon39 c.C6329G p.P2110R GAGACCCTAACTT . 36.0 23.0 47.0 0.0 . 498 . . . none . . PASS Atlas-SNP NCOR1 9611 hgsc.bcm.edu hg19 17 15961343 15961343 + Missense_Mutation SNP G G A rs376750361 alternate_allele TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . NCOR1 NM_006311 exon39 c.C6046T p.H2016Y GATAGTGATGTAA . 78.0 11.0 84.0 0.0 . 240 . . . alt . . PASS Atlas-SNP CCDC103 388389 hgsc.bcm.edu hg19 17 42979927 42979927 + Silent SNP G G A novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . CCDC103 NM_001258395 exon4 c.G471A p.P157P GGGGCCGGCTGAC . 99.0 20.0 102.0 0.0 . 15 . . . none . . PASS Atlas-SNP TEN1 100134934 hgsc.bcm.edu hg19 17 73996327 73996327 + Missense_Mutation SNP G G A rs377039339 TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . TEN1 NM_001113324 exon4 c.G356A p.R119Q AGGAGCGGGGCGG . 92.0 45.0 110.0 0.0 . 4 . . . weak . . PASS Atlas-SNP MIDN 90007 hgsc.bcm.edu hg19 19 1255611 1255611 + Silent SNP T T C novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . MIDN NM_177401 exon7 c.T1047C p.T349T CAGAACTACCTCC . 67.0 25.0 136.0 0.0 . 34 . . . none . . PASS Atlas-SNP SIRPA 140885 hgsc.bcm.edu hg19 20 1903069 1903069 + Missense_Mutation SNP G G C novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . SIRPA NM_001040022 exon5 c.G865C p.E289Q TGGTTGGAGAATG . 278.0 18.0 394.0 0.0 . 83 . . . none . . PASS Atlas-SNP RBM12 10137 hgsc.bcm.edu hg19 20 34240509 34240509 + Silent SNP A A G novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . RBM12 NM_001198840 exon2 c.T2736C p.A912A GACAGCAGCTGTG . 71.0 10.0 97.0 0.0 . 93 . . . none . . PASS Atlas-SNP BCR 613 hgsc.bcm.edu hg19 22 23524065 23524065 + Missense_Mutation SNP G G T novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . BCR NM_021574 exon1 c.G918T p.E306D GCAGGAGAAGCGC . 19.0 11.0 25.0 0.0 . 74 . . . none . . PASS Atlas-SNP UPB1 51733 hgsc.bcm.edu hg19 22 24896185 24896185 + Missense_Mutation SNP T T C novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . UPB1 NM_016327 exon2 c.T215C p.V72A GCATTGTGCACGT . 59.0 14.0 59.0 0.0 . 60 . . . none . . PASS Atlas-SNP RRP7A 27341 hgsc.bcm.edu hg19 22 42912116 42912116 + Silent SNP G G A novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . RRP7A NM_015703 exon3 c.C243T p.T81T GCCACAGGTGGAC . 68.0 14.0 126.0 0.0 . 25 . . . none . . PASS Atlas-SNP PANX2 56666 hgsc.bcm.edu hg19 22 50617455 50617455 + Missense_Mutation SNP C C A novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . PANX2 NM_052839 exon3 c.C1783A p.P595T TCACCTCCCGCCG . 88.0 30.0 142.0 0.0 . 69 . . . none . . PASS Atlas-SNP FAAH2 158584 hgsc.bcm.edu hg19 X 57475117 57475117 + Silent SNP C C G novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . FAAH2 NM_174912 exon10 c.C1389G p.V463V TCATGTCCCTCTA . 69.0 35.0 96.0 0.0 . 66 . . . none . . PASS Atlas-SNP ZCCHC5 203430 hgsc.bcm.edu hg19 X 77913324 77913324 + Silent SNP C C T novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . ZCCHC5 NM_152694 exon2 c.G594A p.Q198Q GAATTCCTGGGCA . 71.0 5.0 67.0 0.0 . 101 . . . none . . PASS Atlas-SNP ND1 10625 hgsc.bcm.edu hg19 MT 3659 3659 + Nonsense_Mutation SNP G G A novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . . ENST00000361390 exon1 c.G353A p.W118X TCCTCTGATCAGG . 178.0 172.0 6.0 0.0 . . . . . none . . PASS Atlas-SNP COX3 5742 hgsc.bcm.edu hg19 MT 9466 9466 + Missense_Mutation SNP T T C novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . . ENST00000362079 exon1 c.T260C p.I87T TATTTATTACCTC . 203.0 198.0 17.0 0.0 . . . . . none . . PASS Atlas-SNP WDR27 253769 hgsc.bcm.edu hg19 6 170038673 170038674 + Frame_Shift_Del DEL TT TT - novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 TT TT . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . WDR27 NM_182552 exon18 c.1831_1832del p.611_611del . . 101.0 21.0 213.0 0.0 . 129 . 0.207921 0 none . . PASS Atlas-INDEL NUP54 53371 hgsc.bcm.edu hg19 4 77053755 77053755 + Frame_Shift_Del DEL T T - novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . NUP54 NM_017426 exon6 c.829delC p.L277fs . . 140.0 33.0 199.0 0.0 . 48 . 0.235714 0 none . . PASS Atlas-Indel,Pindel HELZ 9931 hgsc.bcm.edu hg19 17 65144699 65144700 + Frame_Shift_Ins INS - - T novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . HELZ NM_014877 exon20 c.2607_2608insA p.H869fs . . 134.0 60.0 78.0 0.0 . 160 . 0.447761 0 none . . PASS Atlas-Indel,Pindel MTA1 9112 hgsc.bcm.edu hg19 14 105927224 105927224 + Frame_Shift_Del DEL G G - novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . MTA1 NM_004689 exon10 c.875delA p.E292fs . . 96.0 38.0 166.0 0.0 . 61 . 0.395833 0 none . . PASS Atlas-Indel,Pindel PTPN13 5783 hgsc.bcm.edu hg19 4 87724921 87724947 + In_Frame_Del DEL TCTGGTAAATACACGGGTGCCAACTTA TCTGGTAAATACACGGGTGCCAACTTA - novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 TCTGGTAAATACACGGGTGCCAACTTA TCTGGTAAATACACGGGTGCCAACTTA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . PTPN13 NM_080685 exon43 c.6579_6605del p.2193_2202del . . 73.0 12.0 76.0 0.0 . 203 . 0.164384 0 none . . PASS Atlas-Indel,Pindel WDR27 253769 hgsc.bcm.edu hg19 6 170038676 170038680 + Frame_Shift_Del DEL GCAGG GCAGG - novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 GCAGG GCAGG . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . WDR27 NM_182552 exon18 c.1825_1829del p.609_610del . . 104.0 21.0 214.0 0.0 . 129 . 0.201923 0 none . . PASS Atlas-INDEL ARID4B 51742 hgsc.bcm.edu hg19 1 235416071 235416072 + Frame_Shift_Ins INS - - T novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . ARID4B NM_016374 exon6 c.328_329insA p.G110fs . . 177.0 51.0 210.0 0.0 . 142 . 0.288136 0 none . . PASS Atlas-Indel,Pindel FOXM1 2305 hgsc.bcm.edu hg19 12 2967807 2967812 + In_Frame_Del DEL CTGTAG CTGTAG - novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 CTGTAG CTGTAG . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . FOXM1 NM_202002 exon10 c.2399_2404del p.800_802del . . 44.0 17.0 39.0 0.0 . 62 . 0.386364 0 none . . PASS Atlas-Indel,Pindel ZSCAN5B 342933 hgsc.bcm.edu hg19 19 56701355 56701355 + Frame_Shift_Del DEL G G - novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . ZSCAN5B NM_001080456 exon4 c.1330delT p.C444fs . . 127.0 45.0 156.0 0.0 . 160 . 0.354331 0 none . . PASS Atlas-Indel,Pindel ANKRD52 283373 hgsc.bcm.edu hg19 12 56646601 56646601 + Frame_Shift_Del DEL G G - novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . ANKRD52 NM_173595 exon12 c.1265delT p.L422fs . . 74.0 20.0 80.0 0.0 . 81 . 0.27027 0 none . . PASS Atlas-Indel,Pindel WDR27 253769 hgsc.bcm.edu hg19 6 170038673 170038680 + Frame_Shift_Del DEL TTCGCAGG TTCGCAGG - novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 TTCGCAGG TTCGCAGG . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . WDR27 NM_182552 exon18 c.1825_1832del p.609_611del . . 108.0 22.0 216.0 0.0 . 129 . 0.204 . none . . PASS Pindel ARHGEF19 128272 hgsc.bcm.edu hg19 1 16529006 16529007 + Frame_Shift_Ins INS - - CTCAGGTCCCGCACCTGCAGCTCAGCCAT novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . ARHGEF19 NM_153213 exon13 c.1971_1972insATGGCTGAGCTGCAGGTGCGGGACCTGAG p.S657_L658delinsRWLSCRCGTX . . 163.0 21.0 256.0 0.0 . 49 . 0.129 . none . . PASS Pindel NUDT18 79873 hgsc.bcm.edu hg19 8 21966703 21966708 + Frame_Shift_Del DEL CGCACG CGCACG - novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 CGCACG CGCACG . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . NUDT18 NM_024815 exon2 c.106_110del p.36_37del . . 13.0 10.0 5.0 0.0 . 13 . 0.769 . none . . PASS Pindel PTPLA 9200 hgsc.bcm.edu hg19 10 17659300 17659301 + Frame_Shift_Ins INS - - CCGCTGC novel TCGA-2Z-A9J2-01A-11D-A382-10 TCGA-2Z-A9J2-10A-01D-A385-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 9b136f8d-949c-4f48-9ca6-f9bb90a10bb3 2d763603-a0f5-4dbe-a146-ef518556d752 . PTPLA NM_014241 exon1 c.39_40insGCAGCGG p.G13fs . . 38.0 10.0 50.0 0.0 . 34 . 0.263 . none . . PASS Pindel