From 11494268d1b73a8ac1d8cb71c7b6c5112cd609fa Mon Sep 17 00:00:00 2001 From: Ino de Bruijn Date: Fri, 23 Feb 2018 14:28:09 -0500 Subject: [PATCH] rerun custom isoforms test --- tests/test_output.custom_isoforms.maf | 41 +++++++++++++-------------- 1 file changed, 20 insertions(+), 21 deletions(-) diff --git a/tests/test_output.custom_isoforms.maf b/tests/test_output.custom_isoforms.maf index 626341b..1b08975 100644 --- a/tests/test_output.custom_isoforms.maf +++ b/tests/test_output.custom_isoforms.maf @@ -1,22 +1,21 @@ #version 2.4 -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 HGVSc HGVSp HGVSp_Short Transcript_ID Exon_Number t_depth t_ref_count t_alt_count n_depth n_ref_count n_alt_count all_effects Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation ALLELE_NUM DISTANCE STRAND_VEP SYMBOL SYMBOL_SOURCE HGNC_ID BIOTYPE CANONICAL CCDS ENSP SWISSPROT TREMBL UNIPARC RefSeq SIFT PolyPhen EXON INTRON DOMAINS GMAF AFR_MAF AMR_MAF ASN_MAF EAS_MAF EUR_MAF SAS_MAF AA_MAF EA_MAF CLIN_SIG SOMATIC PUBMED MOTIF_NAME MOTIF_POS HIGH_INF_POS MOTIF_SCORE_CHANGE IMPACT PICK VARIANT_CLASS TSL HGVS_OFFSET PHENO MINIMISED ExAC_AF ExAC_AF_AFR ExAC_AF_AMR ExAC_AF_EAS ExAC_AF_FIN ExAC_AF_NFE ExAC_AF_OTH ExAC_AF_SAS GENE_PHENO FILTER flanking_bps variant_id variant_qual ExAC_AF_Adj ExAC_AC_AN_Adj ExAC_AC_AN ExAC_AC_AN_AFR ExAC_AC_AN_AMR ExAC_AC_AN_EAS ExAC_AC_AN_FIN ExAC_AC_AN_NFE ExAC_AC_AN_OTH ExAC_AC_AN_SAS ExAC_FILTER -MTOR 2475 . GRCh37 1 11290179 11290179 + Intron DEL A A - rs35067541 TUMOR NORMAL A A c.2779+803delT ENST00000361445 20 10 10 35 30 5 MTOR,intron_variant,,ENST00000361445,NM_004958.3;RNU6-291P,downstream_gene_variant,,ENST00000384720,;RPL39P6,upstream_gene_variant,,ENST00000448289,; - ENSG00000198793 ENST00000361445 Transcript intron_variant -/8677 -/7650 -/2549 rs35067541 1 -1 MTOR HGNC 3942 protein_coding YES CCDS127.1 ENSP00000354558 P42345 Q96QW8,B1AKQ2,B1AKP8 UPI000012ABD3 NM_004958.3 18/57 A:0.2985 -:0.3555 -:0.8084 -:0.9137 -:0.7197 -:0.8558 MODIFIER 1 deletion 1 1 . TTAA . . -Unknown 0 . GRCh37 1 15557977 15557978 + IGR DNP TG TG CA novel TUMOR NORMAL TG TG 16 11 5 22 21 1 CA intergenic_variant 1 MODIFIER 1 substitution 1 . GTGG . . -CHD1L 9557 . GRCh37 1 146728217 146728217 + Splice_Site SNP G G A novel TUMOR NORMAL G G c.494+1G>A p.X165_splice ENST00000369258 40 19 21 42 42 0 CHD1L,splice_donor_variant,,ENST00000369258,NM_001256336.1,NM_024568.2,NM_004284.4;CHD1L,splice_donor_variant,,ENST00000431239,;CHD1L,intron_variant,,ENST00000361293,NM_001256337.1;CHD1L,intron_variant,,ENST00000369259,NM_001256338.1;CHD1L,splice_donor_variant,,ENST00000467213,;CHD1L,splice_donor_variant,,ENST00000492728,;CHD1L,intron_variant,,ENST00000488864,;RP11-337C18.10,downstream_gene_variant,,ENST00000606856,; A ENSG00000131778 ENST00000369258 Transcript splice_donor_variant -/2967 494/2694 165/897 1 1 CHD1L HGNC 1916 protein_coding YES CCDS927.1 ENSP00000358262 Q86WJ1 B5MDZ7 UPI000020566F NM_001256336.1,NM_024568.2,NM_004284.4 5/22 HIGH 1 SNV 1 . CGT . . -INHA 3623 . GRCh37 2 220439700 220439701 + Frame_Shift_Ins INS - - CT novel TUMOR NORMAL - - c.562_563dupCT p.Leu189CysfsTer2 p.L189Cfs*2 ENST00000243786 2/2 93 21 72 51 51 0 INHA,frameshift_variant,p.Leu189CysfsTer2,ENST00000243786,NM_002191.3;OBSL1,upstream_gene_variant,,ENST00000404537,NM_015311.2;OBSL1,upstream_gene_variant,,ENST00000265318,;OBSL1,upstream_gene_variant,,ENST00000603926,NM_001173431.1;OBSL1,upstream_gene_variant,,ENST00000373876,;OBSL1,upstream_gene_variant,,ENST00000373873,NM_001173408.1;OBSL1,upstream_gene_variant,,ENST00000289656,;INHA,non_coding_transcript_exon_variant,,ENST00000489456,;OBSL1,upstream_gene_variant,,ENST00000491370,;OBSL1,upstream_gene_variant,,ENST00000465589,;OBSL1,upstream_gene_variant,,ENST00000465149,;,regulatory_region_variant,,ENSR00001715421,; CT ENSG00000123999 ENST00000243786 Transcript frameshift_variant 733-734/1468 553-554/1101 185/366 A/AX gct/gCTct 1 1 INHA HGNC 6065 protein_coding YES CCDS2444.1 ENSP00000243786 P05111 UPI000002C8C6 NM_002191.3 2/2 PIRSF_domain:PIRSF037328,hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF117,Low_complexity_(Seg):seg HIGH 1 insertion 10 1 . TGC . . -BAP1 8314 . GRCh37 3 52437427 52437448 + Splice_Site DEL CCCACCTGTCAGCGCCAGGGGA CCCACCTGTCAGCGCCAGGGGA - novel TUMOR NORMAL CCCACCTGTCAGCGCCAGGGGA CCCACCTGTCAGCGCCAGGGGA c.1713_1729+5delTCCCCTGGCGCTGACAGGTGGG p.X571_splice ENST00000460680 13/17 20 10 10 11 11 0 BAP1,splice_donor_variant,,ENST00000460680,NM_004656.3;BAP1,splice_donor_variant,,ENST00000296288,;BAP1,splice_donor_variant,,ENST00000478368,;BAP1,intron_variant,,ENST00000469613,;DNAH1,downstream_gene_variant,,ENST00000420323,NM_015512.4;BAP1,downstream_gene_variant,,ENST00000470173,;BAP1,splice_donor_variant,,ENST00000466093,;DNAH1,downstream_gene_variant,,ENST00000486752,;DNAH1,downstream_gene_variant,,ENST00000488988,;DNAH1,downstream_gene_variant,,ENST00000490713,;BAP1,downstream_gene_variant,,ENST00000471532,;BAP1,downstream_gene_variant,,ENST00000490804,;BAP1,downstream_gene_variant,,ENST00000483984,;BAP1,downstream_gene_variant,,ENST00000490917,; - ENSG00000163930 ENST00000460680 Transcript splice_donor_variant,coding_sequence_variant,intron_variant 2185-?/3937 1713-?/2190 571-?/729 1 -1 BAP1 HGNC 950 protein_coding YES CCDS2853.1 ENSP00000417132 Q92560 F8WEY5,C9J7L9 UPI0000071B3D NM_004656.3 13/17 13/16 HIGH 1 deletion 1 1 . GGCCCACCTGTCAGCGCCAGGGGAC . . -BAP1 8314 . GRCh37 3 52437702 52437708 + Frame_Shift_Del DEL TGGGTGA TGGGTGA - novel TUMOR NORMAL TGGGTGA TGGGTGA c.1453_1459delTCACCCA p.Ser485ProfsTer84 p.S485Pfs*84 ENST00000460680 13/17 20 10 10 11 11 0 BAP1,frameshift_variant,p.Ser485ProfsTer84,ENST00000460680,NM_004656.3;BAP1,frameshift_variant,p.Ser467ProfsTer84,ENST00000296288,;BAP1,intron_variant,,ENST00000469613,;DNAH1,downstream_gene_variant,,ENST00000420323,NM_015512.4;BAP1,upstream_gene_variant,,ENST00000478368,;BAP1,downstream_gene_variant,,ENST00000470173,;DNAH1,downstream_gene_variant,,ENST00000486752,;DNAH1,downstream_gene_variant,,ENST00000488988,;DNAH1,downstream_gene_variant,,ENST00000490713,;BAP1,upstream_gene_variant,,ENST00000466093,;BAP1,downstream_gene_variant,,ENST00000471532,;BAP1,downstream_gene_variant,,ENST00000490804,;BAP1,downstream_gene_variant,,ENST00000483984,;BAP1,downstream_gene_variant,,ENST00000490917,; - ENSG00000163930 ENST00000460680 Transcript frameshift_variant 1925-1931/3937 1453-1459/2190 485-487/729 SPT/X TCACCCAcc/cc 1 -1 BAP1 HGNC 950 protein_coding YES CCDS2853.1 ENSP00000417132 Q92560 F8WEY5,C9J7L9 UPI0000071B3D NM_004656.3 13/17 hmmpanther:PTHR10589:SF23,hmmpanther:PTHR10589 HIGH 1 deletion 1 1 . GGTGGGTGAG . . -BAP1 8314 . GRCh37 3 52443789 52443850 + Splice_Region DEL TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC - novel TUMOR NORMAL TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC c.38-30_37+8delGGGGACCGGGAGGGCCAGGGGCTGGGGAGGCCGGATGGGCCCGGGACGCGCCTGCCTGACCA ENST00000460680 20 10 10 11 11 0 BAP1,splice_region_variant,,ENST00000460680,NM_004656.3;BAP1,splice_region_variant,,ENST00000296288,;BAP1,5_prime_UTR_variant,,ENST00000470173,;PHF7,upstream_gene_variant,,ENST00000327906,NM_016483.5;PHF7,upstream_gene_variant,,ENST00000347025,NM_001278221.1;PHF7,upstream_gene_variant,,ENST00000461861,;PHF7,upstream_gene_variant,,ENST00000482327,;PHF7,upstream_gene_variant,,ENST00000472337,;BAP1,splice_region_variant,,ENST00000483984,;BAP1,splice_region_variant,,ENST00000490917,;BAP1,upstream_gene_variant,,ENST00000471532,;PHF7,upstream_gene_variant,,ENST00000473145,;BAP1,upstream_gene_variant,,ENST00000490804,;,regulatory_region_variant,,ENSR00001364239,; - ENSG00000163930 ENST00000460680 Transcript splice_region_variant,intron_variant -/3937 -/2190 -/729 1 -1 BAP1 HGNC 950 protein_coding YES CCDS2853.1 ENSP00000417132 Q92560 F8WEY5,C9J7L9 UPI0000071B3D NM_004656.3 1/16 LOW 1 deletion 1 1 . GATGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCCT . . -PIK3CA 5290 . GRCh37 3 178928219 178928220 + In_Frame_Ins INS - - ATA TUMOR NORMAL - - c.1406_1407insTAA p.Glu469delinsAspLys p.E469delinsDK ENST00000263967 9/21 43 21 22 11 11 0 PIK3CA,protein_altering_variant,p.Glu469delinsAspLys,ENST00000263967,NM_006218.2; ATA ENSG00000121879 ENST00000263967 Transcript protein_altering_variant,splice_region_variant 1562-1563/9093 1405-1406/3207 469/1068 E/DK gaa/gATAaa COSM446009,COSM446008 1 1 PIK3CA HGNC 8975 protein_coding YES CCDS43171.1 ENSP00000263967 P42336 Q4LE51,C9JAM9,C9J951 UPI000013D494 NM_006218.2 9/21 PROSITE_profiles:PS51547,hmmpanther:PTHR10048:SF54,hmmpanther:PTHR10048,Pfam_domain:PF00792,Gene3D:2.60.40.150,Superfamily_domains:SSF49562 1,1 MODERATE 1 insertion 1 1,1 1 1 . GGA . . -TERT 7015 . GRCh37 5 1295228 1295228 + 5'Flank SNP G G A novel TUMOR NORMAL G G ENST00000310581 20 10 10 11 11 0 TERT,upstream_gene_variant,,ENST00000310581,NM_198253.2,NM_001193376.1;TERT,upstream_gene_variant,,ENST00000296820,;TERT,upstream_gene_variant,,ENST00000334602,;TERT,upstream_gene_variant,,ENST00000508104,;TERT,upstream_gene_variant,,ENST00000522877,;TERT,upstream_gene_variant,,ENST00000460137,;,regulatory_region_variant,,ENSR00001762748,;,TF_binding_site_variant,,MA0341.1,;,TF_binding_site_variant,,MA0366.1,;,TF_binding_site_variant,,MA0162.2,; A ENSG00000164362 ENST00000310581 Transcript upstream_gene_variant -/4018 -/3399 -/1132 1 66 -1 TERT HGNC 11730 protein_coding YES CCDS3861.2 ENSP00000309572 O14746 Q9UNS6,Q9UNR4,Q9UBR6 UPI0000031309 NM_198253.2,NM_001193376.1 MODIFIER 1 SNV 1 1 . AGG . . -TERT 7015 . GRCh37 5 1295250 1295250 + 5'Flank SNP G G A novel TUMOR NORMAL G G ENST00000310581 20 10 10 11 11 0 TERT,upstream_gene_variant,,ENST00000310581,NM_198253.2,NM_001193376.1;TERT,upstream_gene_variant,,ENST00000296820,;TERT,upstream_gene_variant,,ENST00000334602,;TERT,upstream_gene_variant,,ENST00000508104,;TERT,upstream_gene_variant,,ENST00000522877,;TERT,upstream_gene_variant,,ENST00000460137,;,regulatory_region_variant,,ENSR00001762748,; A ENSG00000164362 ENST00000310581 Transcript upstream_gene_variant -/4018 -/3399 -/1132 1 88 -1 TERT HGNC 11730 protein_coding YES CCDS3861.2 ENSP00000309572 O14746 Q9UNS6,Q9UNR4,Q9UBR6 UPI0000031309 NM_198253.2,NM_001193376.1 MODIFIER 1 SNV 1 1 . GGA . . -MAP3K1 4214 . GRCh37 5 56177849 56177851 + In_Frame_Del DEL CAA CAA - rs5868032 TUMOR NORMAL CAA CAA c.2845_2847delACA p.Thr949del p.T949del ENST00000399503 14/20 50 34 16 46 46 0 MAP3K1,inframe_deletion,p.Thr949del,ENST00000399503,NM_005921.1;MAP3K1,upstream_gene_variant,,ENST00000469188,; - ENSG00000095015 ENST00000399503 Transcript inframe_deletion 2822-2824/7011 2822-2824/4539 941-942/1512 ST/S tCAAca/tca rs5868032 1 1 MAP3K1 HGNC 6848 protein_coding YES CCDS43318.1 ENSP00000382423 Q13233 UPI000015153B NM_005921.1 14/20 Low_complexity_(Seg):seg,hmmpanther:PTHR24361:SF255,hmmpanther:PTHR24361 MODERATE 1 deletion 23 1 0.7315 0.7126 0.5687 0.5597 0.7889 0.7915 0.7258 0.7348 1 common_variant TTCAAC . . 0.7347 74324/101166 77257/105620 5838/8192 6093/10714 4257/7606 5044/6394 41061/51878 479/660 11552/15722 PASS -APC 324 . GRCh37 5 112174758 112174761 + Frame_Shift_Del DEL AAGA AAGA - novel TUMOR NORMAL AAGA AAGA c.3467_3470delAAGA p.Glu1156GlyfsTer8 p.E1156Gfs*8 ENST00000257430 16/16 20 12 8 32 30 2 APC,frameshift_variant,p.Glu1156GlyfsTer8,ENST00000457016,;APC,frameshift_variant,p.Glu1156GlyfsTer8,ENST00000257430,NM_000038.5;APC,frameshift_variant,p.Glu1156GlyfsTer8,ENST00000508376,NM_001127510.2;APC,frameshift_variant,p.Glu1156GlyfsTer8,ENST00000512211,;APC,downstream_gene_variant,,ENST00000507379,NM_001127511.2;APC,downstream_gene_variant,,ENST00000504915,;APC,3_prime_UTR_variant,,ENST00000508624,;APC,non_coding_transcript_exon_variant,,ENST00000502371,;CTC-554D6.1,intron_variant,,ENST00000520401,;APC,downstream_gene_variant,,ENST00000514164,; - ENSG00000134982 ENST00000257430 Transcript frameshift_variant 3523-3526/10701 3467-3470/8532 1156-1157/2843 EE/X gAAGAg/gg 1 1 APC HGNC 583 protein_coding CCDS4107.1 ENSP00000257430 P25054 Q9UM98,Q9P119,Q9HAW6,Q4LE70,E9PFT7,D6RFL6,B2ZRE1,A5HB97,A5HB96,A5HB95,A5HB94,A1YIQ7 UPI000013CF60 NM_000038.5 16/16 Low_complexity_(Seg):seg,hmmpanther:PTHR12607,hmmpanther:PTHR12607:SF11,Pfam_domain:PF05972 HIGH deletion 1 1 . AGAAGAG . . -APC 324 . GRCh37 5 112174758 112174761 + Frame_Shift_Del DEL AAGA AAGA GA novel TUMOR NORMAL AAGA AAGA c.3467_3468delAA p.Glu1156GlyfsTer7 p.E1156Gfs*7 ENST00000257430 16/16 20 12 8 32 30 2 APC,frameshift_variant,p.Glu1156GlyfsTer7,ENST00000457016,;APC,frameshift_variant,p.Glu1156GlyfsTer7,ENST00000257430,NM_000038.5;APC,frameshift_variant,p.Glu1156GlyfsTer7,ENST00000508376,NM_001127510.2;APC,frameshift_variant,p.Glu1156GlyfsTer7,ENST00000512211,;APC,downstream_gene_variant,,ENST00000507379,NM_001127511.2;APC,downstream_gene_variant,,ENST00000504915,;APC,3_prime_UTR_variant,,ENST00000508624,;APC,non_coding_transcript_exon_variant,,ENST00000502371,;CTC-554D6.1,intron_variant,,ENST00000520401,;APC,downstream_gene_variant,,ENST00000514164,; - ENSG00000134982 ENST00000257430 Transcript frameshift_variant 3523-3524/10701 3467-3468/8532 1156/2843 E/X gAA/g 2 1 APC HGNC 583 protein_coding CCDS4107.1 ENSP00000257430 P25054 Q9UM98,Q9P119,Q9HAW6,Q4LE70,E9PFT7,D6RFL6,B2ZRE1,A5HB97,A5HB96,A5HB95,A5HB94,A1YIQ7 UPI000013CF60 NM_000038.5 16/16 Low_complexity_(Seg):seg,hmmpanther:PTHR12607,hmmpanther:PTHR12607:SF11,Pfam_domain:PF05972 HIGH deletion 1 1 . AGAAGAG . . -APC 324 . GRCh37 5 112174758 112174761 + Frame_Shift_Del DEL AAGA GA - novel TUMOR NORMAL - - c.3467_3470delAAGA p.Glu1156GlyfsTer8 p.E1156Gfs*8 ENST00000257430 16/16 20 0 8 32 0 2 APC,frameshift_variant,p.Glu1156GlyfsTer8,ENST00000457016,;APC,frameshift_variant,p.Glu1156GlyfsTer8,ENST00000257430,NM_000038.5;APC,frameshift_variant,p.Glu1156GlyfsTer8,ENST00000508376,NM_001127510.2;APC,frameshift_variant,p.Glu1156GlyfsTer8,ENST00000512211,;APC,downstream_gene_variant,,ENST00000507379,NM_001127511.2;APC,downstream_gene_variant,,ENST00000504915,;APC,3_prime_UTR_variant,,ENST00000508624,;APC,non_coding_transcript_exon_variant,,ENST00000502371,;CTC-554D6.1,intron_variant,,ENST00000520401,;APC,downstream_gene_variant,,ENST00000514164,; - ENSG00000134982 ENST00000257430 Transcript frameshift_variant 3523-3526/10701 3467-3470/8532 1156-1157/2843 EE/X gAAGAg/gg 1 1 APC HGNC 583 protein_coding CCDS4107.1 ENSP00000257430 P25054 Q9UM98,Q9P119,Q9HAW6,Q4LE70,E9PFT7,D6RFL6,B2ZRE1,A5HB97,A5HB96,A5HB95,A5HB94,A1YIQ7 UPI000013CF60 NM_000038.5 16/16 Low_complexity_(Seg):seg,hmmpanther:PTHR12607,hmmpanther:PTHR12607:SF11,Pfam_domain:PF05972 HIGH deletion 1 1 . AGAAGAG . . -APC 324 . GRCh37 5 112174758 112174761 + Frame_Shift_Del DEL AAGA AAGA - novel TUMOR NORMAL AAGA GA c.3467_3470delAAGA p.Glu1156GlyfsTer8 p.E1156Gfs*8 ENST00000257430 16/16 20 12 8 32 30 0 APC,frameshift_variant,p.Glu1156GlyfsTer8,ENST00000457016,;APC,frameshift_variant,p.Glu1156GlyfsTer8,ENST00000257430,NM_000038.5;APC,frameshift_variant,p.Glu1156GlyfsTer8,ENST00000508376,NM_001127510.2;APC,frameshift_variant,p.Glu1156GlyfsTer8,ENST00000512211,;APC,downstream_gene_variant,,ENST00000507379,NM_001127511.2;APC,downstream_gene_variant,,ENST00000504915,;APC,3_prime_UTR_variant,,ENST00000508624,;APC,non_coding_transcript_exon_variant,,ENST00000502371,;CTC-554D6.1,intron_variant,,ENST00000520401,;APC,downstream_gene_variant,,ENST00000514164,; - ENSG00000134982 ENST00000257430 Transcript frameshift_variant 3523-3526/10701 3467-3470/8532 1156-1157/2843 EE/X gAAGAg/gg 1 1 APC HGNC 583 protein_coding CCDS4107.1 ENSP00000257430 P25054 Q9UM98,Q9P119,Q9HAW6,Q4LE70,E9PFT7,D6RFL6,B2ZRE1,A5HB97,A5HB96,A5HB95,A5HB94,A1YIQ7 UPI000013CF60 NM_000038.5 16/16 Low_complexity_(Seg):seg,hmmpanther:PTHR12607,hmmpanther:PTHR12607:SF11,Pfam_domain:PF05972 HIGH deletion 1 1 . AGAAGAG . . -APC 324 . GRCh37 5 112174758 112174761 + Frame_Shift_Del DEL AAGA AAGA GA novel TUMOR NORMAL AAGA - c.3467_3468delAA p.Glu1156GlyfsTer7 p.E1156Gfs*7 ENST00000257430 16/16 20 12 8 32 30 0 APC,frameshift_variant,p.Glu1156GlyfsTer7,ENST00000457016,;APC,frameshift_variant,p.Glu1156GlyfsTer7,ENST00000257430,NM_000038.5;APC,frameshift_variant,p.Glu1156GlyfsTer7,ENST00000508376,NM_001127510.2;APC,frameshift_variant,p.Glu1156GlyfsTer7,ENST00000512211,;APC,downstream_gene_variant,,ENST00000507379,NM_001127511.2;APC,downstream_gene_variant,,ENST00000504915,;APC,3_prime_UTR_variant,,ENST00000508624,;APC,non_coding_transcript_exon_variant,,ENST00000502371,;CTC-554D6.1,intron_variant,,ENST00000520401,;APC,downstream_gene_variant,,ENST00000514164,; - ENSG00000134982 ENST00000257430 Transcript frameshift_variant 3523-3524/10701 3467-3468/8532 1156/2843 E/X gAA/g 2 1 APC HGNC 583 protein_coding CCDS4107.1 ENSP00000257430 P25054 Q9UM98,Q9P119,Q9HAW6,Q4LE70,E9PFT7,D6RFL6,B2ZRE1,A5HB97,A5HB96,A5HB95,A5HB94,A1YIQ7 UPI000013CF60 NM_000038.5 16/16 Low_complexity_(Seg):seg,hmmpanther:PTHR12607,hmmpanther:PTHR12607:SF11,Pfam_domain:PF05972 HIGH deletion 1 1 . AGAAGAG . . -CCND3 896 . GRCh37 6 41903782 41903783 + Missense_Mutation DNP AG AG CA rs386700585 TUMOR NORMAL AG AG c.774_775delCTinsTG p.Ser259Ala p.S259A ENST00000372991 5/5 50 28 22 48 48 0 CCND3,missense_variant,p.Ser178Ala,ENST00000511642,;CCND3,missense_variant,p.Ser209Ala,ENST00000372987,NM_001287427.1;CCND3,missense_variant,p.Ser178Ala,ENST00000372988,NM_001136017.2;CCND3,missense_variant,p.Ser259Ala,ENST00000372991,NM_001760.3;CCND3,missense_variant,p.Ser63Ala,ENST00000415497,NM_001136126.1;CCND3,missense_variant,p.Ser187Ala,ENST00000414200,NM_001136125.1;CCND3,missense_variant,p.Leu132Cys,ENST00000510503,;BYSL,downstream_gene_variant,,ENST00000230340,NM_004053.3;CCND3,downstream_gene_variant,,ENST00000512426,;CCND3,downstream_gene_variant,,ENST00000508143,;CCND3,downstream_gene_variant,,ENST00000502771,;CCND3,downstream_gene_variant,,ENST00000505064,;CCND3,downstream_gene_variant,,ENST00000514588,;CCND3,non_coding_transcript_exon_variant,,ENST00000511686,;CCND3,downstream_gene_variant,,ENST00000513956,;CCND3,downstream_gene_variant,,ENST00000514382,;CCND3,downstream_gene_variant,,ENST00000506555,;BYSL,downstream_gene_variant,,ENST00000372996,;BYSL,downstream_gene_variant,,ENST00000489290,;CCND3,downstream_gene_variant,,ENST00000505672,;CCND3,downstream_gene_variant,,ENST00000510058,;CCND3,downstream_gene_variant,,ENST00000505884,;CCND3,downstream_gene_variant,,ENST00000511161,; CA ENSG00000112576 ENST00000372991 Transcript missense_variant 973-974/2085 774-775/879 258-259/292 AS/AA gcCTct/gcTGct rs386700585 1 -1 CCND3 HGNC 1585 protein_coding YES CCDS4863.1 ENSP00000362082 P30281 D6RIX2,D6RDL3 UPI00001275C9 NM_001760.3 5/5 hmmpanther:PTHR10177:SF65,hmmpanther:PTHR10177,Pfam_domain:PF02984,PIRSF_domain:PIRSF001771 MODERATE 1 substitution 1 0.5389 0.8059 0.4456 0.5308 0.5457 0.5447 0.5058 0.4557 common_variant GAGG . . 0.5419 56771/104760 57238/106204 7268/9018 4895/10984 4118/7758 3512/6436 29293/53774 346/684 7339/16106 PASS -MET 4233 . GRCh37 7 116412043 116412043 + Missense_Mutation SNP G G C novel TUMOR NORMAL G G c.3028G>C p.Asp1010His p.D1010H ENST00000397752 14/21 47 25 22 99 98 1 MET,missense_variant,p.Asp1010His,ENST00000397752,NM_000245.2,NM_001127500.1;MET,missense_variant,p.Asp1028His,ENST00000318493,;MET,intron_variant,,ENST00000454623,;MET,downstream_gene_variant,,ENST00000422097,;,regulatory_region_variant,,ENSR00001800475,; C ENSG00000105976 ENST00000397752 Transcript missense_variant,splice_region_variant 3228/6635 3028/4173 1010/1390 D/H Gat/Cat 1 1 MET HGNC 7029 protein_coding CCDS43636.1 ENSP00000380860 P08581 Q9UEJ3,B4DPY6,B4DLF5 UPI000020F975 NM_000245.2,NM_001127500.1 deleterious(0.02) probably_damaging(0.976) 14/21 hmmpanther:PTHR24416:SF261,hmmpanther:PTHR24416,PIRSF_domain:PIRSF000617 MODERATE SNV 1 1 . AGG . . -FLT3 2322 . GRCh37 13 28608242 28608243 + In_Frame_Ins INS - - ACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTACCCCCTCGGGGGG novel TUMOR NORMAL - - c.1813_1814insCCCCCCGAGGGGGTAATGAGTACTTCTACGTTGATTTCAGAGAATATGAATATGATCTCAAATGGGAGT p.Glu604_Phe605insSerProArgGlyGlyAsnGluTyrPheTyrValAspPheArgGluTyrGluTyrAspLeuLysTrpGlu p.E604_F605insSPRGGNEYFYVDFREYEYDLKWE ENST00000241453 14/24 20 10 10 11 11 0 FLT3,inframe_insertion,p.Glu604_Phe605insSerProArgGlyGlyAsnGluTyrPheTyrValAspPheArgGluTyrGluTyrAspLeuLysTrpGlu,ENST00000380982,;FLT3,inframe_insertion,p.Glu604_Phe605insSerProArgGlyGlyAsnGluTyrPheTyrValAspPheArgGluTyrGluTyrAspLeuLysTrpGlu,ENST00000241453,NM_004119.2;FLT3,inframe_insertion,p.Glu604_Phe605insSerProArgGlyGlyAsnGluTyrPheTyrValAspPheArgGluTyrGluTyrAspLeuLysTrpGlu,ENST00000537084,;FLT3,inframe_insertion,p.Glu604_Phe605insSerProArgGlyGlyAsnGluTyrPheTyrValAspPheArgGluTyrGluTyrAspLeuLysTrpGlu,ENST00000380987,; ACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTACCCCCTCGGGGGG ENSG00000122025 ENST00000241453 Transcript inframe_insertion 1895-1896/3842 1813-1814/2982 605/993 F/SPRGGNEYFYVDFREYEYDLKWEF ttt/tCCCCCCGAGGGGGTAATGAGTACTTCTACGTTGATTTCAGAGAATATGAATATGATCTCAAATGGGAGTtt 1 -1 FLT3 HGNC 3765 protein_coding YES CCDS31953.1 ENSP00000241453 P36888 UPI00001FC90B NM_004119.2 14/24 Gene3D:3.30.200.20,PIRSF_domain:PIRSF000615,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF278,Superfamily_domains:SSF56112 MODERATE 1 insertion 1 1 . AAA . . -TP53 7157 . GRCh37 17 7579312 7579312 + Splice_Region SNP C C A rs55863639 TUMOR NORMAL C C c.375G>T p.= p.T125T ENST00000269305 4/11 42 20 22 19 18 1 TP53,splice_region_variant,p.=,ENST00000420246,NM_001126114.2,NM_001276696.1;TP53,splice_region_variant,p.=,ENST00000455263,NM_001276695.1,NM_001126113.2;TP53,splice_region_variant,p.=,ENST00000269305,NM_001126112.2,NM_001276761.1,NM_001276760.1,NM_000546.5,NM_001126118.1;TP53,splice_region_variant,p.=,ENST00000445888,;TP53,splice_region_variant,p.=,ENST00000359597,;TP53,splice_region_variant,p.=,ENST00000413465,;TP53,splice_region_variant,p.=,ENST00000508793,;TP53,splice_region_variant,p.=,ENST00000604348,;TP53,splice_region_variant,p.=,ENST00000503591,;TP53,intron_variant,,ENST00000509690,;TP53,intron_variant,,ENST00000514944,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,splice_region_variant,,ENST00000505014,;TP53,upstream_gene_variant,,ENST00000510385,;TP53,upstream_gene_variant,,ENST00000504290,;TP53,upstream_gene_variant,,ENST00000504937,; A ENSG00000141510 ENST00000269305 Transcript splice_region_variant,synonymous_variant 565/2579 375/1182 125/393 T acG/acT rs55863639,TP53_g.11606G>T,COSM45940,COSM381995,COSM381996,COSM3388231,COSM1638003 1 -1 TP53 HGNC 11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 S5LQU8,Q761V2,Q6IT77,Q1HGV1,Q0PKT5,L0ES54,L0EQ05,K7PPA8,H2EHT1,G4Y083,E9PCY9,E7ESS1,E7EMR6,B5AKF6,B4DNI2,A4GWD0,A4GWB8,A4GWB5,A4GW97,A4GW76,A4GW75,A4GW74,A4GW67,A2I9Z1,A2I9Z0 UPI000002ED67 NM_001126112.2,NM_001276761.1,NM_001276760.1,NM_000546.5,NM_001126118.1 4/11 Gene3D:2.60.40.720,Pfam_domain:PF00870,Prints_domain:PR00386,hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Superfamily_domains:SSF49417 pathogenic 0,0,1,1,1,1,1 25730903 LOW 1 SNV 1,0,1,1,1,1,1 1 1 . CCG . . +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 HGVSc HGVSp HGVSp_Short Transcript_ID Exon_Number t_depth t_ref_count t_alt_count n_depth n_ref_count n_alt_count all_effects Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation ALLELE_NUM DISTANCE STRAND_VEP SYMBOL SYMBOL_SOURCE HGNC_ID BIOTYPE CANONICAL CCDS ENSP SWISSPROT TREMBL UNIPARC RefSeq SIFT PolyPhen EXON INTRON DOMAINS GMAF AFR_MAF AMR_MAF ASN_MAF EAS_MAF EUR_MAF SAS_MAF AA_MAF EA_MAF CLIN_SIG SOMATIC PUBMED MOTIF_NAME MOTIF_POS HIGH_INF_POS MOTIF_SCORE_CHANGE IMPACT PICK VARIANT_CLASS TSL HGVS_OFFSET PHENO MINIMISED ExAC_AF ExAC_AF_AFR ExAC_AF_AMR ExAC_AF_EAS ExAC_AF_FIN ExAC_AF_NFE ExAC_AF_OTH ExAC_AF_SAS GENE_PHENO FILTER flanking_bps variant_id variant_qual ExAC_AF_Adj ExAC_AC_AN_Adj ExAC_AC_AN ExAC_AC_AN_AFR ExAC_AC_AN_AMR ExAC_AC_AN_EAS ExAC_AC_AN_FIN ExAC_AC_AN_NFE ExAC_AC_AN_OTH ExAC_AC_AN_SAS ExAC_FILTER Caller +MTOR 2475 . GRCh37 1 11290179 11290179 + Intron DEL A A - rs35067541 TUMOR NORMAL A A c.2779+803delT ENST00000361445 20 10 10 35 30 5 MTOR,intron_variant,,ENST00000361445,NM_004958.3;RNU6-291P,downstream_gene_variant,,ENST00000384720,;RPL39P6,upstream_gene_variant,,ENST00000448289,; - ENSG00000198793 ENST00000361445 Transcript intron_variant -/8677 -/7650 -/2549 rs35067541 1 -1 MTOR HGNC 3942 protein_coding YES CCDS127.1 ENSP00000354558 MTOR_HUMAN Q96QW8_HUMAN,B1AKQ2_HUMAN,B1AKP8_HUMAN UPI000012ABD3 NM_004958.3 18/57 A:0.2985 -:0.3555 -:0.8084 -:0.9137 -:0.7197 -:0.8558 MODIFIER 1 deletion 1 . TTAA . . +Unknown 0 . GRCh37 1 15557977 15557978 + IGR DNP TG TG CA novel TUMOR NORMAL TG TG 16 11 5 22 21 1 CA intergenic_variant 1 MODIFIER 1 substitution 1 . GTGG . . +CHD1L 9557 . GRCh37 1 146728217 146728217 + Splice_Site SNP G G A novel TUMOR NORMAL G G c.494+1G>A p.X165_splice ENST00000369258 40 19 21 42 42 0 CHD1L,splice_donor_variant,,ENST00000369258,NM_001256336.1,NM_024568.2,NM_004284.4;CHD1L,splice_donor_variant,,ENST00000431239,;CHD1L,intron_variant,,ENST00000361293,NM_001256337.1;CHD1L,intron_variant,,ENST00000369259,NM_001256338.1;CHD1L,splice_donor_variant,,ENST00000467213,;CHD1L,splice_donor_variant,,ENST00000492728,;CHD1L,intron_variant,,ENST00000488864,;RP11-337C18.10,downstream_gene_variant,,ENST00000606856,; A ENSG00000131778 ENST00000369258 Transcript splice_donor_variant -/2967 494/2694 165/897 1 1 CHD1L HGNC 1916 protein_coding YES CCDS927.1 ENSP00000358262 CHD1L_HUMAN B5MDZ7_HUMAN UPI000020566F NM_001256336.1,NM_024568.2,NM_004284.4 5/22 HIGH 1 SNV 1 . CGT . . +INHA 3623 . GRCh37 2 220439700 220439701 + Frame_Shift_Ins INS - - CT novel TUMOR NORMAL - - c.562_563dupCT p.Leu189CysfsTer2 p.L189Cfs*2 ENST00000243786 2/2 93 21 72 51 51 0 INHA,frameshift_variant,p.Leu189CysfsTer2,ENST00000243786,NM_002191.3;OBSL1,upstream_gene_variant,,ENST00000404537,NM_015311.2;OBSL1,upstream_gene_variant,,ENST00000265318,;OBSL1,upstream_gene_variant,,ENST00000603926,NM_001173431.1;OBSL1,upstream_gene_variant,,ENST00000373876,;OBSL1,upstream_gene_variant,,ENST00000373873,NM_001173408.1;OBSL1,upstream_gene_variant,,ENST00000289656,;INHA,non_coding_transcript_exon_variant,,ENST00000489456,;OBSL1,upstream_gene_variant,,ENST00000491370,;OBSL1,upstream_gene_variant,,ENST00000465589,;OBSL1,upstream_gene_variant,,ENST00000465149,;,regulatory_region_variant,,ENSR00001715421,; CT ENSG00000123999 ENST00000243786 Transcript frameshift_variant 733-734/1468 553-554/1101 185/366 A/AX gct/gCTct 1 1 INHA HGNC 6065 protein_coding YES CCDS2444.1 ENSP00000243786 INHA_HUMAN UPI000002C8C6 NM_002191.3 2/2 Low_complexity_(Seg):seg,PTHR11848,PTHR11848:SF117,PIRSF_domain:PIRSF037328 HIGH 1 insertion 10 1 . TGC . . +BAP1 8314 . GRCh37 3 52437427 52437448 + Splice_Site DEL CCCACCTGTCAGCGCCAGGGGA CCCACCTGTCAGCGCCAGGGGA - novel TUMOR NORMAL CCCACCTGTCAGCGCCAGGGGA CCCACCTGTCAGCGCCAGGGGA c.1713_1729+5delTCCCCTGGCGCTGACAGGTGGG p.X571_splice ENST00000460680 13/17 20 10 10 11 11 0 BAP1,splice_donor_variant,,ENST00000460680,NM_004656.3;BAP1,splice_donor_variant,,ENST00000296288,;BAP1,splice_donor_variant,,ENST00000478368,;BAP1,intron_variant,,ENST00000469613,;DNAH1,downstream_gene_variant,,ENST00000420323,NM_015512.4;BAP1,downstream_gene_variant,,ENST00000470173,;BAP1,splice_donor_variant,,ENST00000466093,;DNAH1,downstream_gene_variant,,ENST00000486752,;DNAH1,downstream_gene_variant,,ENST00000488988,;DNAH1,downstream_gene_variant,,ENST00000490713,;BAP1,downstream_gene_variant,,ENST00000471532,;BAP1,downstream_gene_variant,,ENST00000490804,;BAP1,downstream_gene_variant,,ENST00000483984,;BAP1,downstream_gene_variant,,ENST00000490917,; - ENSG00000163930 ENST00000460680 Transcript splice_donor_variant,coding_sequence_variant,intron_variant 2185-?/3937 1713-?/2190 571-?/729 1 -1 BAP1 HGNC 950 protein_coding YES CCDS2853.1 ENSP00000417132 BAP1_HUMAN F8WEY5_HUMAN,C9J7L9_HUMAN UPI0000071B3D NM_004656.3 13/17 13/16 HIGH 1 deletion 1 . GGCCCACCTGTCAGCGCCAGGGGAC . . +BAP1 8314 . GRCh37 3 52437702 52437708 + Frame_Shift_Del DEL TGGGTGA TGGGTGA - novel TUMOR NORMAL TGGGTGA TGGGTGA c.1453_1459delTCACCCA p.Ser485ProfsTer84 p.S485Pfs*84 ENST00000460680 13/17 20 10 10 11 11 0 BAP1,frameshift_variant,p.Ser485ProfsTer84,ENST00000460680,NM_004656.3;BAP1,frameshift_variant,p.Ser467ProfsTer84,ENST00000296288,;BAP1,intron_variant,,ENST00000469613,;DNAH1,downstream_gene_variant,,ENST00000420323,NM_015512.4;BAP1,upstream_gene_variant,,ENST00000478368,;BAP1,downstream_gene_variant,,ENST00000470173,;DNAH1,downstream_gene_variant,,ENST00000486752,;DNAH1,downstream_gene_variant,,ENST00000488988,;DNAH1,downstream_gene_variant,,ENST00000490713,;BAP1,upstream_gene_variant,,ENST00000466093,;BAP1,downstream_gene_variant,,ENST00000471532,;BAP1,downstream_gene_variant,,ENST00000490804,;BAP1,downstream_gene_variant,,ENST00000483984,;BAP1,downstream_gene_variant,,ENST00000490917,; - ENSG00000163930 ENST00000460680 Transcript frameshift_variant 1925-1931/3937 1453-1459/2190 485-487/729 SPT/X TCACCCAcc/cc 1 -1 BAP1 HGNC 950 protein_coding YES CCDS2853.1 ENSP00000417132 BAP1_HUMAN F8WEY5_HUMAN,C9J7L9_HUMAN UPI0000071B3D NM_004656.3 13/17 PTHR10589:SF23,PTHR10589 HIGH 1 deletion 1 . GGTGGGTGAG . . +BAP1 8314 . GRCh37 3 52443789 52443850 + Splice_Region DEL TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC - novel TUMOR NORMAL TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC c.38-30_37+8delGGGGACCGGGAGGGCCAGGGGCTGGGGAGGCCGGATGGGCCCGGGACGCGCCTGCCTGACCA ENST00000460680 20 10 10 11 11 0 BAP1,splice_region_variant,,ENST00000460680,NM_004656.3;BAP1,splice_region_variant,,ENST00000296288,;BAP1,5_prime_UTR_variant,,ENST00000470173,;PHF7,upstream_gene_variant,,ENST00000327906,NM_016483.5;PHF7,upstream_gene_variant,,ENST00000347025,NM_001278221.1;PHF7,upstream_gene_variant,,ENST00000461861,;PHF7,upstream_gene_variant,,ENST00000482327,;PHF7,upstream_gene_variant,,ENST00000472337,;BAP1,splice_region_variant,,ENST00000483984,;BAP1,splice_region_variant,,ENST00000490917,;BAP1,upstream_gene_variant,,ENST00000471532,;PHF7,upstream_gene_variant,,ENST00000473145,;BAP1,upstream_gene_variant,,ENST00000490804,;,regulatory_region_variant,,ENSR00001364239,; - ENSG00000163930 ENST00000460680 Transcript splice_region_variant,intron_variant -/3937 -/2190 -/729 1 -1 BAP1 HGNC 950 protein_coding YES CCDS2853.1 ENSP00000417132 BAP1_HUMAN F8WEY5_HUMAN,C9J7L9_HUMAN UPI0000071B3D NM_004656.3 1/16 LOW 1 deletion 1 . GATGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCCT . . +PIK3CA 5290 . GRCh37 3 178928219 178928220 + In_Frame_Ins INS - - ATA TUMOR NORMAL - - c.1406_1407insTAA p.Glu469delinsAspLys p.E469delinsDK ENST00000263967 9/21 43 21 22 11 11 0 PIK3CA,protein_altering_variant,p.Glu469delinsAspLys,ENST00000263967,NM_006218.2; ATA ENSG00000121879 ENST00000263967 Transcript protein_altering_variant,splice_region_variant 1562-1563/9093 1405-1406/3207 469/1068 E/DK gaa/gATAaa COSM446009,COSM446008 1 1 PIK3CA HGNC 8975 protein_coding YES CCDS43171.1 ENSP00000263967 PK3CA_HUMAN Q4LE51_HUMAN,C9JAM9_HUMAN,C9J951_HUMAN UPI000013D494 NM_006218.2 9/21 PROSITE_profiles:PS51547,PTHR10048:SF54,PTHR10048,Pfam_domain:PF00792,2.60.40.150,Superfamily_domains:SSF49562 1,1 MODERATE 1 insertion 1 1,1 1 . GGA . . +TERT 7015 . GRCh37 5 1295228 1295228 + 5'Flank SNP G G A novel TUMOR NORMAL G G ENST00000310581 20 10 10 11 11 0 TERT,upstream_gene_variant,,ENST00000310581,NM_198253.2,NM_001193376.1;TERT,upstream_gene_variant,,ENST00000296820,;TERT,upstream_gene_variant,,ENST00000334602,;TERT,upstream_gene_variant,,ENST00000508104,;TERT,upstream_gene_variant,,ENST00000522877,;TERT,upstream_gene_variant,,ENST00000460137,;,regulatory_region_variant,,ENSR00001762748,;,TF_binding_site_variant,,MA0341.1,;,TF_binding_site_variant,,MA0366.1,;,TF_binding_site_variant,,MA0162.2,; A ENSG00000164362 ENST00000310581 Transcript upstream_gene_variant -/4018 -/3399 -/1132 1 66 -1 TERT HGNC 11730 protein_coding YES CCDS3861.2 ENSP00000309572 TERT_HUMAN Q9UNS6_HUMAN,Q9UNR4_HUMAN,Q9UBR6_HUMAN UPI0000031309 NM_198253.2,NM_001193376.1 MODIFIER 1 SNV 1 . AGG . . +TERT 7015 . GRCh37 5 1295250 1295250 + 5'Flank SNP G G A novel TUMOR NORMAL G G ENST00000310581 20 10 10 11 11 0 TERT,upstream_gene_variant,,ENST00000310581,NM_198253.2,NM_001193376.1;TERT,upstream_gene_variant,,ENST00000296820,;TERT,upstream_gene_variant,,ENST00000334602,;TERT,upstream_gene_variant,,ENST00000508104,;TERT,upstream_gene_variant,,ENST00000522877,;TERT,upstream_gene_variant,,ENST00000460137,;,regulatory_region_variant,,ENSR00001762748,; A ENSG00000164362 ENST00000310581 Transcript upstream_gene_variant -/4018 -/3399 -/1132 1 88 -1 TERT HGNC 11730 protein_coding YES CCDS3861.2 ENSP00000309572 TERT_HUMAN Q9UNS6_HUMAN,Q9UNR4_HUMAN,Q9UBR6_HUMAN UPI0000031309 NM_198253.2,NM_001193376.1 MODIFIER 1 SNV 1 . GGA . . +MAP3K1 4214 . GRCh37 5 56177849 56177851 + In_Frame_Del DEL CAA CAA - rs5868032 TUMOR NORMAL CAA CAA c.2845_2847delACA p.Thr949del p.T949del ENST00000399503 14/20 50 34 16 46 46 0 MAP3K1,inframe_deletion,p.Thr949del,ENST00000399503,NM_005921.1;MAP3K1,upstream_gene_variant,,ENST00000469188,; - ENSG00000095015 ENST00000399503 Transcript inframe_deletion 2822-2824/7011 2822-2824/4539 941-942/1512 ST/S tCAAca/tca rs5868032 1 1 MAP3K1 HGNC 6848 protein_coding YES CCDS43318.1 ENSP00000382423 M3K1_HUMAN UPI000015153B NM_005921.1 14/20 Low_complexity_(Seg):seg,PTHR24361:SF255,PTHR24361 MODERATE 1 deletion 23 1 0.7315 0.7126 0.5687 0.5597 0.7889 0.7915 0.7258 0.7348 common_variant TTCAAC . . 0.7347 74324/101166 77257/105620 5838/8192 6093/10714 4257/7606 5044/6394 41061/51878 479/660 11552/15722 PASS +APC 324 . GRCh37 5 112174758 112174761 + Frame_Shift_Del DEL AAGA AAGA - TUMOR NORMAL AAGA AAGA c.3467_3470delAAGA p.Glu1156GlyfsTer8 p.E1156Gfs*8 ENST00000508376 17/17 20 12 8 32 30 2 APC,frameshift_variant,p.Glu1156GlyfsTer8,ENST00000457016,;APC,frameshift_variant,p.Glu1156GlyfsTer8,ENST00000257430,NM_000038.5;APC,frameshift_variant,p.Glu1156GlyfsTer8,ENST00000508376,NM_001127510.2;APC,frameshift_variant,p.Glu1156GlyfsTer8,ENST00000512211,;APC,downstream_gene_variant,,ENST00000507379,NM_001127511.2;APC,downstream_gene_variant,,ENST00000504915,;APC,3_prime_UTR_variant,,ENST00000508624,;APC,non_coding_transcript_exon_variant,,ENST00000502371,;CTC-554D6.1,intron_variant,,ENST00000520401,;APC,downstream_gene_variant,,ENST00000514164,; - ENSG00000134982 ENST00000508376 Transcript frameshift_variant 3624-3627/10619 3467-3470/8532 1156-1157/2843 EE/X gAAGAg/gg COSM19217 1 1 APC HGNC 583 protein_coding CCDS4107.1 ENSP00000427089 APC_HUMAN Q9UM98_HUMAN,Q9P119_HUMAN,Q9HAW6_HUMAN,Q4LE70_HUMAN,E9PFT7_HUMAN,D6RFL6_HUMAN,B2ZRE1_HUMAN,A5HB97_HUMAN,A5HB96_HUMAN,A5HB95_HUMAN,A5HB94_HUMAN,A1YIQ7_HUMAN UPI000013CF60 NM_001127510.2 17/17 Low_complexity_(Seg):seg,PTHR12607,PTHR12607:SF11,Pfam_domain:PF05972 1 HIGH deletion 1 1 . AGAAGAG . . +APC 324 . GRCh37 5 112174758 112174761 + Frame_Shift_Del DEL AAGA AAGA GA novel TUMOR NORMAL AAGA AAGA c.3467_3468delAA p.Glu1156GlyfsTer7 p.E1156Gfs*7 ENST00000508376 17/17 20 12 8 32 30 2 APC,frameshift_variant,p.Glu1156GlyfsTer7,ENST00000457016,;APC,frameshift_variant,p.Glu1156GlyfsTer7,ENST00000257430,NM_000038.5;APC,frameshift_variant,p.Glu1156GlyfsTer7,ENST00000508376,NM_001127510.2;APC,frameshift_variant,p.Glu1156GlyfsTer7,ENST00000512211,;APC,downstream_gene_variant,,ENST00000507379,NM_001127511.2;APC,downstream_gene_variant,,ENST00000504915,;APC,3_prime_UTR_variant,,ENST00000508624,;APC,non_coding_transcript_exon_variant,,ENST00000502371,;CTC-554D6.1,intron_variant,,ENST00000520401,;APC,downstream_gene_variant,,ENST00000514164,; - ENSG00000134982 ENST00000508376 Transcript frameshift_variant 3624-3625/10619 3467-3468/8532 1156/2843 E/X gAA/g 1 1 APC HGNC 583 protein_coding CCDS4107.1 ENSP00000427089 APC_HUMAN Q9UM98_HUMAN,Q9P119_HUMAN,Q9HAW6_HUMAN,Q4LE70_HUMAN,E9PFT7_HUMAN,D6RFL6_HUMAN,B2ZRE1_HUMAN,A5HB97_HUMAN,A5HB96_HUMAN,A5HB95_HUMAN,A5HB94_HUMAN,A1YIQ7_HUMAN UPI000013CF60 NM_001127510.2 17/17 Low_complexity_(Seg):seg,PTHR12607,PTHR12607:SF11,Pfam_domain:PF05972 HIGH deletion 1 . AGAAGAG . . +APC 324 . GRCh37 5 112174758 112174761 + Frame_Shift_Del DEL AAGA AAGA GA novel TUMOR NORMAL - AAGA c.3467_3468delAA p.Glu1156GlyfsTer7 p.E1156Gfs*7 ENST00000508376 17/17 20 12 8 32 30 0 APC,frameshift_variant,p.Glu1156GlyfsTer7,ENST00000457016,;APC,frameshift_variant,p.Glu1156GlyfsTer7,ENST00000257430,NM_000038.5;APC,frameshift_variant,p.Glu1156GlyfsTer7,ENST00000508376,NM_001127510.2;APC,frameshift_variant,p.Glu1156GlyfsTer7,ENST00000512211,;APC,downstream_gene_variant,,ENST00000507379,NM_001127511.2;APC,downstream_gene_variant,,ENST00000504915,;APC,3_prime_UTR_variant,,ENST00000508624,;APC,non_coding_transcript_exon_variant,,ENST00000502371,;CTC-554D6.1,intron_variant,,ENST00000520401,;APC,downstream_gene_variant,,ENST00000514164,; - ENSG00000134982 ENST00000508376 Transcript frameshift_variant 3624-3625/10619 3467-3468/8532 1156/2843 E/X gAA/g 1 1 APC HGNC 583 protein_coding CCDS4107.1 ENSP00000427089 APC_HUMAN Q9UM98_HUMAN,Q9P119_HUMAN,Q9HAW6_HUMAN,Q4LE70_HUMAN,E9PFT7_HUMAN,D6RFL6_HUMAN,B2ZRE1_HUMAN,A5HB97_HUMAN,A5HB96_HUMAN,A5HB95_HUMAN,A5HB94_HUMAN,A1YIQ7_HUMAN UPI000013CF60 NM_001127510.2 17/17 Low_complexity_(Seg):seg,PTHR12607,PTHR12607:SF11,Pfam_domain:PF05972 HIGH deletion 1 . AGAAGAG . . +APC 324 . GRCh37 5 112174758 112174761 + Frame_Shift_Del DEL AAGA AAGA - novel TUMOR NORMAL GA AAGA c.3467_3470delAAGA p.Glu1156GlyfsTer8 p.E1156Gfs*8 ENST00000508376 17/17 20 12 8 32 30 0 APC,frameshift_variant,p.Glu1156GlyfsTer8,ENST00000457016,;APC,frameshift_variant,p.Glu1156GlyfsTer8,ENST00000257430,NM_000038.5;APC,frameshift_variant,p.Glu1156GlyfsTer8,ENST00000508376,NM_001127510.2;APC,frameshift_variant,p.Glu1156GlyfsTer8,ENST00000512211,;APC,downstream_gene_variant,,ENST00000507379,NM_001127511.2;APC,downstream_gene_variant,,ENST00000504915,;APC,3_prime_UTR_variant,,ENST00000508624,;APC,non_coding_transcript_exon_variant,,ENST00000502371,;CTC-554D6.1,intron_variant,,ENST00000520401,;APC,downstream_gene_variant,,ENST00000514164,; - ENSG00000134982 ENST00000508376 Transcript frameshift_variant 3624-3627/10619 3467-3470/8532 1156-1157/2843 EE/X gAAGAg/gg 1 1 APC HGNC 583 protein_coding CCDS4107.1 ENSP00000427089 APC_HUMAN Q9UM98_HUMAN,Q9P119_HUMAN,Q9HAW6_HUMAN,Q4LE70_HUMAN,E9PFT7_HUMAN,D6RFL6_HUMAN,B2ZRE1_HUMAN,A5HB97_HUMAN,A5HB96_HUMAN,A5HB95_HUMAN,A5HB94_HUMAN,A1YIQ7_HUMAN UPI000013CF60 NM_001127510.2 17/17 Low_complexity_(Seg):seg,PTHR12607,PTHR12607:SF11,Pfam_domain:PF05972 HIGH deletion 1 . AGAAGAG . . +CCND3 896 . GRCh37 6 41903782 41903783 + Missense_Mutation DNP AG AG CA rs386700585 TUMOR NORMAL AG AG c.774_775delCTinsTG p.Ser259Ala p.S259A ENST00000372991 5/5 50 28 22 48 48 0 CCND3,missense_variant,p.Ser178Ala,ENST00000511642,;CCND3,missense_variant,p.Ser209Ala,ENST00000372987,NM_001287427.1;CCND3,missense_variant,p.Ser178Ala,ENST00000372988,NM_001136017.2;CCND3,missense_variant,p.Ser259Ala,ENST00000372991,NM_001760.3;CCND3,missense_variant,p.Ser63Ala,ENST00000415497,NM_001136126.1;CCND3,missense_variant,p.Ser187Ala,ENST00000414200,NM_001136125.1;CCND3,missense_variant,p.Leu132Cys,ENST00000510503,;BYSL,downstream_gene_variant,,ENST00000230340,NM_004053.3;CCND3,downstream_gene_variant,,ENST00000512426,;CCND3,downstream_gene_variant,,ENST00000508143,;CCND3,downstream_gene_variant,,ENST00000502771,;CCND3,downstream_gene_variant,,ENST00000505064,;CCND3,downstream_gene_variant,,ENST00000514588,;CCND3,non_coding_transcript_exon_variant,,ENST00000511686,;CCND3,downstream_gene_variant,,ENST00000513956,;CCND3,downstream_gene_variant,,ENST00000514382,;CCND3,downstream_gene_variant,,ENST00000506555,;BYSL,downstream_gene_variant,,ENST00000372996,;BYSL,downstream_gene_variant,,ENST00000489290,;CCND3,downstream_gene_variant,,ENST00000505672,;CCND3,downstream_gene_variant,,ENST00000510058,;CCND3,downstream_gene_variant,,ENST00000505884,;CCND3,downstream_gene_variant,,ENST00000511161,; CA ENSG00000112576 ENST00000372991 Transcript missense_variant 973-974/2085 774-775/879 258-259/292 AS/AA gcCTct/gcTGct rs386700585 1 -1 CCND3 HGNC 1585 protein_coding YES CCDS4863.1 ENSP00000362082 CCND3_HUMAN D6RIX2_HUMAN,D6RDL3_HUMAN UPI00001275C9 NM_001760.3 5/5 PTHR10177:SF65,PTHR10177,Pfam_domain:PF02984,PIRSF_domain:PIRSF001771 MODERATE 1 substitution 1 0.5389 0.8059 0.4456 0.5308 0.5457 0.5447 0.5058 0.4557 common_variant GAGG . . 0.5419 56771/104760 57238/106204 7268/9018 4895/10984 4118/7758 3512/6436 29293/53774 346/684 7339/16106 PASS +MET 4233 . GRCh37 7 116412043 116412043 + Missense_Mutation SNP G G C novel TUMOR NORMAL G G c.3028G>C p.Asp1010His p.D1010H ENST00000397752 14/21 47 25 22 99 98 1 MET,missense_variant,p.Asp1010His,ENST00000397752,NM_000245.2,NM_001127500.1;MET,missense_variant,p.Asp1028His,ENST00000318493,;MET,intron_variant,,ENST00000454623,;MET,downstream_gene_variant,,ENST00000422097,;,regulatory_region_variant,,ENSR00001800475,; C ENSG00000105976 ENST00000397752 Transcript missense_variant,splice_region_variant 3228/6635 3028/4173 1010/1390 D/H Gat/Cat 1 1 MET HGNC 7029 protein_coding CCDS43636.1 ENSP00000380860 MET_HUMAN Q9UEJ3_HUMAN,B4DPY6_HUMAN,B4DLF5_HUMAN UPI000020F975 NM_000245.2,NM_001127500.1 deleterious(0.02) probably_damaging(0.976) 14/21 PTHR24416:SF261,PTHR24416,PIRSF_domain:PIRSF000617 MODERATE SNV 1 . AGG . . +FLT3 2322 . GRCh37 13 28608242 28608243 + In_Frame_Ins INS - - ACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTACCCCCTCGGGGGG novel TUMOR NORMAL - - c.1813_1814insCCCCCCGAGGGGGTAATGAGTACTTCTACGTTGATTTCAGAGAATATGAATATGATCTCAAATGGGAGT p.Glu604_Phe605insSerProArgGlyGlyAsnGluTyrPheTyrValAspPheArgGluTyrGluTyrAspLeuLysTrpGlu p.E604_F605insSPRGGNEYFYVDFREYEYDLKWE ENST00000241453 14/24 20 10 10 11 11 0 FLT3,inframe_insertion,p.Glu604_Phe605insSerProArgGlyGlyAsnGluTyrPheTyrValAspPheArgGluTyrGluTyrAspLeuLysTrpGlu,ENST00000380982,;FLT3,inframe_insertion,p.Glu604_Phe605insSerProArgGlyGlyAsnGluTyrPheTyrValAspPheArgGluTyrGluTyrAspLeuLysTrpGlu,ENST00000241453,NM_004119.2;FLT3,inframe_insertion,p.Glu604_Phe605insSerProArgGlyGlyAsnGluTyrPheTyrValAspPheArgGluTyrGluTyrAspLeuLysTrpGlu,ENST00000537084,;FLT3,inframe_insertion,p.Glu604_Phe605insSerProArgGlyGlyAsnGluTyrPheTyrValAspPheArgGluTyrGluTyrAspLeuLysTrpGlu,ENST00000380987,; ACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTACCCCCTCGGGGGG ENSG00000122025 ENST00000241453 Transcript inframe_insertion 1895-1896/3842 1813-1814/2982 605/993 F/SPRGGNEYFYVDFREYEYDLKWEF ttt/tCCCCCCGAGGGGGTAATGAGTACTTCTACGTTGATTTCAGAGAATATGAATATGATCTCAAATGGGAGTtt 1 -1 FLT3 HGNC 3765 protein_coding YES CCDS31953.1 ENSP00000241453 FLT3_HUMAN UPI00001FC90B NM_004119.2 14/24 Superfamily_domains:SSF56112,PIRSF_domain:PIRSF000615,3.30.200.20,PTHR24416:SF278,PTHR24416 MODERATE 1 insertion 1 . AAA . . +TP53 7157 . GRCh37 17 7579312 7579312 + Splice_Region SNP C C A rs55863639 TUMOR NORMAL C C c.375G>T p.= p.T125T ENST00000269305 4/11 42 20 22 19 18 1 TP53,splice_region_variant,p.=,ENST00000420246,NM_001126114.2,NM_001276696.1;TP53,splice_region_variant,p.=,ENST00000455263,NM_001276695.1,NM_001126113.2;TP53,splice_region_variant,p.=,ENST00000269305,NM_001126112.2,NM_001276761.1,NM_001276760.1,NM_000546.5,NM_001126118.1;TP53,splice_region_variant,p.=,ENST00000445888,;TP53,splice_region_variant,p.=,ENST00000359597,;TP53,splice_region_variant,p.=,ENST00000413465,;TP53,splice_region_variant,p.=,ENST00000508793,;TP53,splice_region_variant,p.=,ENST00000604348,;TP53,splice_region_variant,p.=,ENST00000503591,;TP53,intron_variant,,ENST00000509690,;TP53,intron_variant,,ENST00000514944,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,splice_region_variant,,ENST00000505014,;TP53,upstream_gene_variant,,ENST00000510385,;TP53,upstream_gene_variant,,ENST00000504290,;TP53,upstream_gene_variant,,ENST00000504937,; A ENSG00000141510 ENST00000269305 Transcript splice_region_variant,synonymous_variant 565/2579 375/1182 125/393 T acG/acT rs55863639,TP53_g.11606G>T,COSM45940,COSM381995,COSM381996,COSM3388231,COSM1638003 1 -1 TP53 HGNC 11998 protein_coding YES CCDS11118.1 ENSP00000269305 P53_HUMAN S5LQU8_HUMAN,Q761V2_HUMAN,Q6IT77_HUMAN,Q1HGV1_HUMAN,Q0PKT5_HUMAN,L0ES54_HUMAN,L0EQ05_HUMAN,K7PPA8_HUMAN,H2EHT1_HUMAN,G4Y083_HUMAN,E9PCY9_HUMAN,E7ESS1_HUMAN,E7EMR6_HUMAN,B5AKF6_HUMAN,B4DNI2_HUMAN,A4GWD0_HUMAN,A4GWB8_HUMAN,A4GWB5_HUMAN,A4GW97_HUMAN,A4GW76_HUMAN,A4GW75_HUMAN,A4GW74_HUMAN,A4GW67_HUMAN,A2I9Z1_HUMAN,A2I9Z0_HUMAN UPI000002ED67 NM_001126112.2,NM_001276761.1,NM_001276760.1,NM_000546.5,NM_001126118.1 4/11 PTHR11447:SF6,PTHR11447,Pfam_domain:PF00870,2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386 pathogenic 0,0,1,1,1,1,1 25730903 LOW 1 SNV 1,0,1,1,1,1,1 1 . CCG . .