#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
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	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_NormalRefReads_WU	i_NormalVAF_WU	i_NormalVarReads_WU	i_ORegAnno_bin	i_RNARefReads_WU	i_RNAVAF_WU	i_RNAVarReads_WU	i_Start_position_hg18	i_TumorRefReads_WU	i_TumorVAF_WU	i_TumorVarReads_WU	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_deletion_substructures	i_domain	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_name	i_gene_type	i_havana_transcript	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_type	i_ucsc_cons	i_variant
NRAS	4893	genome.wustl.edu	37	1	115258744	115258744	+	Missense_Mutation	SNP	C	C	T	rs121434596		TCGA-AB-2967-03A-01D-0739-09	TCGA-AB-2967-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	60a69167-464f-4df2-a6f9-ed402ed58f76	b5babadf-7b10-45fc-8c93-5f68a08b07ed	g.chr1:115258744C>T	ENST00000369535.4	-	2	291	c.38G>A	c.(37-39)gGt>gAt	p.G13D	CSDE1_ENST00000483407.1_5'Flank	NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	13			G -> D (in ALPS4). {ECO:0000269|PubMed:17517660}.|G -> R (in CMNS and colorectal cancer; somatic mutation). {ECO:0000269|PubMed:18633438, ECO:0000269|PubMed:3102434}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G13D(188)|p.G13V(56)|p.G13A(16)|p.G13N(1)|p.G13Y(1)		NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTTCCCAACACCACCTGCTCC	0.498	G13D(HDMYZ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G13D(KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G13D(MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G13D(NCIH929_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G13V(AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	50	Mis		"""melanoma, MM, AML, thyroid"""				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																												dbGAP		Dom	yes		1	1p13.2	4893	neuroblastoma RAS viral (v-ras) oncogene homolog		"""L, E"""	262	Substitution - Missense(262)	haematopoietic_and_lymphoid_tissue(217)|skin(36)|thyroid(2)|large_intestine(2)|soft_tissue(2)|central_nervous_system(1)|endometrium(1)|NS(1)	1	GRCh37	CM071907	NRAS	M	rs121434596						208.0	185.0	193.0					1																	115258744		2203	4300	6503	115060267	SO:0001583	missense	0	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.38G>A	1.37:g.115258744C>T	ENSP00000358548:p.Gly13Asp	1990	8.49	185		22	12.00	3	115060267	643	45.98	549	Q14971|Q15104|Q15282	Missense_Mutation	SNP	HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases	p.G13D	ENST00000369535.4	37	c.38	CCDS877.1	1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.048221	0.93740	.	.	ENSG00000213281	ENST00000369535	T	0.72942	-0.7	5.58	5.58	0.84498	Small GTP-binding protein domain (1);	0.000000	0.56097	U	0.000022	T	0.79644	0.4481	M	0.92604	3.325	0.80722	D	1	B	0.33964	0.434	B	0.42319	0.383	T	0.81673	-0.0826	10	0.62326	D	0.03	.	19.3769	0.94514	0.0:1.0:0.0:0.0	.	13	P01111	RASN_HUMAN	D	13	ENSP00000358548:G13D	ENSP00000358548:G13D	G	-	2	0	NRAS	115060267	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.651000	0.83577	2.906000	0.99361	0.655000	0.94253	GGT	-	HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases		0.498	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NRAS	protein_coding	OTTHUMT00000033395.2	C	NM_002524		115060267	-1	no_errors	NM_002524.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
DNMT3A	1788	genome.wustl.edu	37	2	25468163	25468163	+	Nonsense_Mutation	SNP	C	C	A	rs373860660		TCGA-AB-2967-03A-01D-0739-09	TCGA-AB-2967-11A-01D-0739-09	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	60a69167-464f-4df2-a6f9-ed402ed58f76	b5babadf-7b10-45fc-8c93-5f68a08b07ed	g.chr2:25468163C>A	ENST00000264709.3	-	13	1850	c.1513G>T	c.(1513-1515)Gaa>Taa	p.E505*	DNMT3A_ENST00000474887.1_5'Flank|DNMT3A_ENST00000321117.5_Nonsense_Mutation_p.E505*|DNMT3A_ENST00000402667.1_Nonsense_Mutation_p.E282*|DNMT3A_ENST00000380746.4_Nonsense_Mutation_p.E316*	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	505	ADD. {ECO:0000255|PROSITE- ProRule:PRU00865}.|Interaction with the PRC2/EED-EZH2 complex. {ECO:0000250}.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)	p.E505*(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGGGGGTGTTCCAGGGTAACA	0.622			"""Mis, F, N, S"""		AML																																	dbGAP		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	1	Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(1)	2						C	stop/GLU,stop/GLU,stop/GLU	0,4406		0,0,2203	93.0	90.0	91.0		1513,946,1513	5.3	1.0	2		91	1,8599		0,1,4299	no	stop-gained,stop-gained,stop-gained	DNMT3A	NM_022552.3,NM_153759.2,NM_175629.1	,,	0,1,6502	AA,AC,CC		0.0116,0.0,0.0077	,,	505/913,316/724,505/913	25468163	1,13005	2203	4300	6503	25321667	SO:0001587	stop_gained	0				CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.1513G>T	2.37:g.25468163C>A	ENSP00000264709:p.Glu505*	664	6.57	47		8	46.67	7	25321667	113	54.22	135	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Nonsense_Mutation	SNP	HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT	p.E505*	ENST00000264709.3	37	c.1513	CCDS33157.1	2	.	.	.	.	.	.	.	.	.	.	C	40	7.942861	0.98574	0.0	1.16E-4	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	.	.	.	5.27	5.27	0.74061	.	0.051571	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	-8.8259	16.4462	0.83935	0.0:1.0:0.0:0.0	.	.	.	.	X	316;505;505;282	.	ENSP00000264709:E505X	E	-	1	0	DNMT3A	25321667	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.975000	0.49281	2.735000	0.93741	0.655000	0.94253	GAA	-	NULL		0.622	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	DNMT3A	protein_coding	OTTHUMT00000211587.1	C	NM_022552		25321667	-1	no_errors	NM_022552.3	genbank	human	reviewed	54_36p	nonsense	SNP	1.000	A
COLQ	8292	genome.wustl.edu	37	3	15504577	15504577	+	Intron	SNP	C	C	A			TCGA-AB-2967-03A-01D-0739-09	TCGA-AB-2967-11A-01D-0739-09	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	60a69167-464f-4df2-a6f9-ed402ed58f76	b5babadf-7b10-45fc-8c93-5f68a08b07ed	g.chr3:15504577C>A	ENST00000383788.5	-	12	940				COLQ_ENST00000435459.2_Intron|COLQ_ENST00000383786.5_Intron|COLQ_ENST00000383781.4_Intron|COLQ_ENST00000383785.2_Intron|COLQ_ENST00000383787.2_Intron|COLQ_ENST00000603808.1_Intron	NM_005677.3	NP_005668.2	Q9Y215	COLQ_HUMAN	collagen-like tail subunit (single strand of homotrimer) of asymmetric acetylcholinesterase						acetylcholine catabolic process in synaptic cleft (GO:0001507)|asymmetric protein localization (GO:0008105)	basal lamina (GO:0005605)|cell junction (GO:0030054)|collagen trimer (GO:0005581)|extracellular space (GO:0005615)|synapse (GO:0045202)				endometrium(2)|large_intestine(4)|lung(10)|skin(3)	19						GATTGCAATACACCGAAGACA	0.567																																						dbGAP											0			3																																								15479581	SO:0001627	intron_variant	0			AF057036	CCDS33709.1, CCDS43057.1, CCDS46768.1	3p	2008-07-18			ENSG00000206561	ENSG00000206561			2226	protein-coding gene	gene with protein product	"""single strand of homotrimeric collagen-like tail subunit of asymmetric acetylcholinesterase"", ""collagenic tail of endplate acetylcholinesterase"", ""AChE Q subunit"", ""acetylcholinesterase-associated collagen"""	603033				9689136	Standard	NM_005677		Approved	EAD	uc003bzx.3	Q9Y215	OTTHUMG00000156233	ENST00000383788.5:c.814+3270G>T	3.37:g.15504577C>A		1812	8.59	171		2	0.00	0	15479581	514	45.80	436	B3KY09|Q6DK18|Q6YH18|Q6YH19|Q6YH20|Q6YH21|Q9NP18|Q9NP19|Q9NP20|Q9NP21|Q9NP22|Q9NP23|Q9NP24|Q9UP88	Silent	SNP	NULL	p.V25	ENST00000383788.5	37	c.75	CCDS33709.1	3																																																																																			-	NULL		0.567	COLQ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	LOC100128342	protein_coding	OTTHUMT00000343575.1	C	NM_005677		15479581	-1	no_errors	XM_001721613.1	genbank	human	model	54_36p	silent	SNP	0.000	A
LRRC2	79442	genome.wustl.edu	37	3	46574399	46574399	+	Splice_Site	SNP	C	C	T			TCGA-AB-2967-03A-01D-0739-09	TCGA-AB-2967-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	60a69167-464f-4df2-a6f9-ed402ed58f76	b5babadf-7b10-45fc-8c93-5f68a08b07ed	g.chr3:46574399C>T	ENST00000395905.3	-	5	883	c.491G>A	c.(490-492)gGt>gAt	p.G164D	LRRC2_ENST00000296144.3_Splice_Site_p.G164D	NM_024512.4	NP_078788.2	Q9BYS8	LRRC2_HUMAN	leucine rich repeat containing 2	164								p.G164D(1)		breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	17		Ovarian(412;0.0563)		OV - Ovarian serous cystadenocarcinoma(275;6.37e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00133)|KIRC - Kidney renal clear cell carcinoma(197;0.0214)|Kidney(197;0.0254)		CTTCAAACAACCTGTCAGCAG	0.358																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	3											85.0	84.0	84.0					3																	46574399		2203	4300	6503	46549403	SO:0001630	splice_region_variant	0			AJ308569	CCDS2741.1	3p21.3	2014-07-30	2003-11-19		ENSG00000163827	ENSG00000163827			14676	protein-coding gene	gene with protein product		607180	"""leucine-rich repeat-containing 2"""			11896456	Standard	NM_024512		Approved		uc010hji.3	Q9BYS8	OTTHUMG00000133479	ENST00000395905.3:c.491-1G>A	3.37:g.46574399C>T		1882	7.05	143		NA	NA	NA	46549403	327	47.93	301	B2RDQ7|Q96LT5	Missense_Mutation	SNP	HMMPfam_LRR_1,HMMSmart_LRR_TYP,superfamily_SSF52058	p.G164D	ENST00000395905.3	37	c.491	CCDS2741.1	3	.	.	.	.	.	.	.	.	.	.	C	19.21	3.783812	0.70222	.	.	ENSG00000163827	ENST00000395905;ENST00000296144	T;T	0.38401	1.14;1.14	4.88	4.88	0.63580	.	0.000000	0.64402	D	0.000001	T	0.46171	0.1379	M	0.71206	2.165	0.53688	D	0.999975	P	0.47484	0.896	P	0.46629	0.522	T	0.49826	-0.8898	10	0.54805	T	0.06	.	15.9442	0.79782	0.0:1.0:0.0:0.0	.	164	Q9BYS8	LRRC2_HUMAN	D	164	ENSP00000379241:G164D;ENSP00000296144:G164D	ENSP00000296144:G164D	G	-	2	0	LRRC2	46549403	1.000000	0.71417	0.953000	0.39169	0.940000	0.58332	6.525000	0.73795	2.707000	0.92482	0.563000	0.77884	GGT	-	superfamily_SSF52058		0.358	LRRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LRRC2	protein_coding	OTTHUMT00000257375.2	C		Missense_Mutation	46549403	-1	no_errors	NM_024512.3	genbank	human	validated	54_36p	missense	SNP	0.998	T
OR8A1	390275	genome.wustl.edu	37	11	124440298	124440298	+	Missense_Mutation	SNP	G	G	A	rs371661396		TCGA-AB-2967-03A-01D-0739-09	TCGA-AB-2967-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	60a69167-464f-4df2-a6f9-ed402ed58f76	b5babadf-7b10-45fc-8c93-5f68a08b07ed	g.chr11:124440298G>A	ENST00000284287.3	+	1	406	c.334G>A	c.(334-336)Gca>Aca	p.A112T		NM_001005194.1	NP_001005194.1	Q8NGG7	OR8A1_HUMAN	olfactory receptor, family 8, subfamily A, member 1	112					axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A112T(1)		haematopoietic_and_lymphoid_tissue(1)|lung(16)|ovary(2)|prostate(1)|skin(2)	22		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0214)		CATCTCCTACGCAGGGTGCAT	0.473																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	11						G	THR/ALA	1,4401	2.1+/-5.4	0,1,2200	175.0	154.0	161.0		334	0.9	0.8	11		161	0,8598		0,0,4299	no	missense	OR8A1	NM_001005194.1	58	0,1,6499	AA,AG,GG		0.0,0.0227,0.0077	benign	112/327	124440298	1,12999	2201	4299	6500	123945508	SO:0001583	missense	0			BK004495	CCDS31712.1	11q24.2	2012-08-09			ENSG00000196119	ENSG00000196119		"""GPCR / Class A : Olfactory receptors"""	8469	protein-coding gene	gene with protein product							Standard	NM_001005194		Approved	OST025	uc010san.2	Q8NGG7	OTTHUMG00000165923	ENST00000284287.3:c.334G>A	11.37:g.124440298G>A	ENSP00000284287:p.Ala112Thr	2444	8.14	217		NA	NA	NA	123945508	844	51.38	893	Q6IEW7|Q96RC6	Missense_Mutation	SNP	HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321	p.A112T	ENST00000284287.3	37	c.334	CCDS31712.1	11	.	.	.	.	.	.	.	.	.	.	G	11.53	1.666773	0.29604	2.27E-4	0.0	ENSG00000196119	ENST00000284287	T	0.00397	7.57	5.03	0.892	0.19230	GPCR, rhodopsin-like superfamily (1);	0.825771	0.10096	N	0.716602	T	0.00144	0.0004	N	0.10629	0.01	0.18873	N	0.999985	B	0.09022	0.002	B	0.09377	0.004	T	0.07366	-1.0776	10	0.14252	T	0.57	.	5.1886	0.15197	0.0755:0.1229:0.5499:0.2517	.	112	Q8NGG7	OR8A1_HUMAN	T	112	ENSP00000284287:A112T	ENSP00000284287:A112T	A	+	1	0	OR8A1	123945508	0.000000	0.05858	0.837000	0.33122	0.939000	0.58152	-2.715000	0.00815	0.688000	0.31529	0.650000	0.86243	GCA	-	HMMPfam_7tm_1,superfamily_SSF81321		0.473	OR8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR8A1	protein_coding	OTTHUMT00000387062.1	G	NM_001005194		123945508	+1	no_errors	NM_001005194.1	genbank	human	provisional	54_36p	missense	SNP	0.008	A
GRIP1	23426	genome.wustl.edu	37	12	66838485	66838485	+	Silent	SNP	G	G	A			TCGA-AB-2967-03A-01D-0739-09	TCGA-AB-2967-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	60a69167-464f-4df2-a6f9-ed402ed58f76	b5babadf-7b10-45fc-8c93-5f68a08b07ed	g.chr12:66838485G>A	ENST00000398016.3	-	12	1478	c.1410C>T	c.(1408-1410)gaC>gaT	p.D470D	GRIP1_ENST00000286445.7_Silent_p.D522D|GRIP1_ENST00000359742.4_Silent_p.D522D	NM_021150.3	NP_066973.2	Q96DT0	LEG12_HUMAN	glutamate receptor interacting protein 1	0					intrinsic apoptotic signaling pathway (GO:0097193)	nucleus (GO:0005634)	lactose binding (GO:0030395)	p.D470D(1)		NS(3)|breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(19)|ovary(2)|prostate(2)|skin(1)	50			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		CCATCACTCTGTCTCCAATCT	0.468																																						dbGAP											1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	12											124.0	118.0	120.0					12																	66838485		1955	4146	6101	65124752	SO:0001819	synonymous_variant	0			AJ133439	CCDS41807.1	12q13.13	2008-05-02			ENSG00000155974	ENSG00000155974			18708	protein-coding gene	gene with protein product		604597				10197531	Standard	NM_021150		Approved		uc001stk.3	Q9Y3R0	OTTHUMG00000169019	ENST00000398016.3:c.1410C>T	12.37:g.66838485G>A		1289	10.72	155		NA	NA	NA	65124752	554	51.40	587	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Silent	SNP	HMMPfam_PDZ,HMMSmart_SM00228,superfamily_PDZ domain-like	p.D470	ENST00000398016.3	37	c.1410	CCDS41807.1	12	.	.	.	.	.	.	.	.	.	.	G	8.687	0.906602	0.17833	.	.	ENSG00000155974	ENST00000538164	.	.	.	5.69	2.89	0.33648	.	.	.	.	.	T	0.60983	0.2311	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55179	-0.8181	4	.	.	.	-20.1828	10.8328	0.46669	0.1973:0.0:0.8027:0.0	.	.	.	.	I	337	.	.	T	-	2	0	GRIP1	65124752	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.918000	0.56432	0.350000	0.24002	0.539000	0.68188	ACA	-	HMMPfam_PDZ,HMMSmart_SM00228,superfamily_PDZ domain-like		0.468	GRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GRIP1	protein_coding	OTTHUMT00000401975.2	G			65124752	-1	no_errors	NM_021150.2	genbank	human	validated	54_36p	silent	SNP	1.000	A
FAM57B	83723	genome.wustl.edu	37	16	30037136	30037136	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AB-2967-03A-01D-0739-09	TCGA-AB-2967-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	60a69167-464f-4df2-a6f9-ed402ed58f76	b5babadf-7b10-45fc-8c93-5f68a08b07ed	g.chr16:30037136G>A	ENST00000380495.4	-	4	1182	c.451C>T	c.(451-453)Cga>Tga	p.R151*	FAM57B_ENST00000564806.1_Nonsense_Mutation_p.R101*|FAM57B_ENST00000279389.4_Nonsense_Mutation_p.R101*	NM_031478.4	NP_113666.2	Q71RH2	FA57B_HUMAN	family with sequence similarity 57, member B	151	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				ceramide biosynthetic process (GO:0046513)|negative regulation of fat cell differentiation (GO:0045599)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sphingosine N-acyltransferase activity (GO:0050291)	p.R151*(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(1)	14						TTACCCTGTCGCCACACCTGG	0.602																																						dbGAP											1	Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(1)	16											98.0	94.0	96.0					16																	30037136		2197	4300	6497	29944637	SO:0001587	stop_gained	0			AF370365	CCDS10667.2	16p11.2	2013-02-19			ENSG00000149926	ENSG00000149926			25295	protein-coding gene	gene with protein product		615175				11230166, 23275342	Standard	NM_031478		Approved	DKFZP434I2117	uc002dvt.3	Q71RH2	OTTHUMG00000132105	ENST00000380495.4:c.451C>T	16.37:g.30037136G>A	ENSP00000369863:p.Arg151*	467	9.81	51		0	100.00	1	29944637	89	45.83	77	Q9H0J1	Nonsense_Mutation	SNP	HMMPfam_TRAM_LAG1_CLN8,HMMSmart_SM00724	p.R151*	ENST00000380495.4	37	c.451	CCDS10667.2	16	.	.	.	.	.	.	.	.	.	.	G	41	8.979373	0.99023	.	.	ENSG00000149926	ENST00000380495	.	.	.	5.17	4.2	0.49525	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06494	T	0.89	-2.6091	12.0718	0.53620	0.0:0.0:0.6892:0.3108	.	.	.	.	X	151	.	ENSP00000369863:R151X	R	-	1	2	FAM57B	29944637	1.000000	0.71417	1.000000	0.80357	0.791000	0.44710	1.706000	0.37878	1.145000	0.42336	0.561000	0.74099	CGA	-	HMMPfam_TRAM_LAG1_CLN8,HMMSmart_SM00724		0.602	FAM57B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	FAM57B	protein_coding	OTTHUMT00000255142.2	G	NM_031478		29944637	-1	no_errors	NM_031478.4	genbank	human	validated	54_36p	nonsense	SNP	1.000	A
HYDIN	54768	genome.wustl.edu	37	16	70874027	70874027	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2967-03A-01D-0739-09	TCGA-AB-2967-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	60a69167-464f-4df2-a6f9-ed402ed58f76	b5babadf-7b10-45fc-8c93-5f68a08b07ed	g.chr16:70874027G>A	ENST00000393567.2	-	76	13133	c.12983C>T	c.(12982-12984)gCt>gTt	p.A4328V		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	4328					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.A4327V(1)|p.A4279V(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				GGGCATCCCAGCTTGATAGAT	0.478																																						dbGAP											2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	16											4.0	4.0	4.0					16																	70874027		1464	3617	5081	69431528	SO:0001583	missense	0			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.12983C>T	16.37:g.70874027G>A	ENSP00000377197:p.Ala4328Val	2183	3.74	85		NA	NA	NA	69431528	1603	20.28	408	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	superfamily_PapD-like,superfamily_P-loop containing nucleoside triphosphate hydrolases	p.A4327V	ENST00000393567.2	37	c.12980	CCDS59269.1	16	.	.	.	.	.	.	.	.	.	.	G	32	5.161009	0.94727	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.00949	5.51	5.59	5.59	0.84812	.	0.000000	0.32736	U	0.005714	T	0.04048	0.0113	M	0.62723	1.935	0.80722	D	1	D	0.56968	0.978	P	0.58266	0.836	T	0.53767	-0.8392	10	0.42905	T	0.14	.	19.1717	0.93580	0.0:0.0:1.0:0.0	.	4327	F8WD23	.	V	4328;4327	ENSP00000377197:A4328V	ENSP00000313052:A4327V	A	-	2	0	HYDIN	69431528	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	8.446000	0.90329	2.634000	0.89283	0.505000	0.49811	GCT	-	superfamily_PapD-like		0.478	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	HYDIN	protein_coding	OTTHUMT00000398624.3	G			69431528	-1	no_errors	NM_032821.2	genbank	human	validated	54_36p	missense	SNP	1.000	A
SEMA4A	64218	genome.wustl.edu	37	1	156126203	156126204	+	Splice_Site	DEL	AG	AG	-			TCGA-AB-2967-03A-01D-0739-09	TCGA-AB-2967-11A-01D-0739-09	AG	AG	AG	-	AG	AG	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	60a69167-464f-4df2-a6f9-ed402ed58f76	b5babadf-7b10-45fc-8c93-5f68a08b07ed	g.chr1:156126203_156126204delAG	ENST00000368285.3	+	3	406		c.e3-1		SEMA4A_ENST00000355014.2_Splice_Site|SEMA4A_ENST00000368286.2_Splice_Site|SEMA4A_ENST00000368284.1_Splice_Site|SEMA4A_ENST00000368282.1_Splice_Site	NM_001193300.1|NM_022367.3	NP_001180229.1|NP_071762.2	Q9H3S1	SEM4A_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A						angiogenesis (GO:0001525)|axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|regulation of cell shape (GO:0008360)|regulation of endothelial cell migration (GO:0010594)|semaphorin-plexin signaling pathway (GO:0071526)|T-helper 1 cell differentiation (GO:0045063)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|ovary(2)|skin(2)	5	Hepatocellular(266;0.158)					CTCCTCCAACAGGGGATGAACG	0.545																																						dbGAP											0			1																																								154392828	SO:0001630	splice_region_variant	0			AK022416	CCDS1132.1, CCDS53378.1	1q22	2014-01-28			ENSG00000196189	ENSG00000196189		"""Semaphorins"""	10729	protein-coding gene	gene with protein product		607292		SEMAB		7748561	Standard	NM_022367		Approved	SemB, FLJ12287, CORD10	uc009wrq.3	Q9H3S1	OTTHUMG00000014042	ENST00000368285.3:c.140-1AG>-	1.37:g.156126203_156126204delAG		0	7.02	160		0	12.50	2	154392827	0	43.40	240	B2RDH8|B3KR76|Q5TCI5|Q5TCJ6|Q8WUA9	Splice_Site	DEL	-	e2-1	ENST00000368285.3	37	c.140-2_140-1	CCDS1132.1	1																																																																																			-	-		0.545	SEMA4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SEMA4A	protein_coding	OTTHUMT00000039484.2	AG	NM_022367	Intron	154392828	+1	no_errors	NM_022367.2	genbank	human	provisional	54_36p	splice_site_del	DEL	0.852:0.849	-
NPM1	4869	genome.wustl.edu	37	5	170837547	170837548	+	Frame_Shift_Ins	INS	-	-	TCTG			TCGA-AB-2967-03A-01D-0739-09	TCGA-AB-2967-11A-01D-0739-09	-	-	-	TCTG	-	-	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	60a69167-464f-4df2-a6f9-ed402ed58f76	b5babadf-7b10-45fc-8c93-5f68a08b07ed	g.chr5:170837547_170837548insTCTG	ENST00000296930.5	+	11	1164_1165	c.863_864insTCTG	c.(862-867)tggcagfs	p.WQ288fs	NPM1_ENST00000351986.6_Frame_Shift_Ins_p.WQ259fs|NPM1_ENST00000517671.1_Frame_Shift_Ins_p.WQ288fs	NM_002520.6	NP_002511.1	P06748	NPM_HUMAN	nucleophosmin (nucleolar phosphoprotein B23, numatrin)	288	Required for nucleolar localization.			WQWRKSL -> CLAVEEVSLRK (in Ref. 6; AAW67752/AAW67755). {ECO:0000305}.|WQWRKSL -> CMAVEEVSLRK (in Ref. 6; AAW67753 and 7; ABC40399). {ECO:0000305}.|WQWRKSL -> CVAVEEVSLRK (in Ref. 6; AAW67754). {ECO:0000305}.	cell aging (GO:0007569)|CENP-A containing nucleosome assembly (GO:0034080)|centrosome cycle (GO:0007098)|DNA repair (GO:0006281)|intracellular protein transport (GO:0006886)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of centrosome duplication (GO:0010826)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|nucleocytoplasmic transport (GO:0006913)|nucleosome assembly (GO:0006334)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of translation (GO:0045727)|protein localization (GO:0008104)|protein oligomerization (GO:0051259)|regulation of centriole replication (GO:0046599)|regulation of eIF2 alpha phosphorylation by dsRNA (GO:0060735)|regulation of endodeoxyribonuclease activity (GO:0032071)|regulation of endoribonuclease activity (GO:0060699)|response to stress (GO:0006950)|ribosome assembly (GO:0042255)|signal transduction (GO:0007165)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle pole centrosome (GO:0031616)	histone binding (GO:0042393)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)|ribosomal large subunit binding (GO:0043023)|ribosomal small subunit binding (GO:0043024)|RNA binding (GO:0003723)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|unfolded protein binding (GO:0051082)	p.W288fs*12(2114)|p.W288fs*10(9)|p.Q289fs*11(3)|p.W288*(1)	NPM1/ALK(632)	central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4261)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	4269	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CAAGATCTCTGGCAGTGGAGGA	0.312			"""T, F """	"""ALK, RARA, MLF1"""	"""NHL, APL, AML"""																																	dbGAP		Dom	yes		5	5q35	4869	"""nucleophosmin (nucleolar phosphoprotein B23, numatrin)"""		L	2127	Insertion - Frameshift(2118)|Complex - frameshift(8)|Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(2127)	5																																								170770153	SO:0001589	frameshift_variant	0			M26697	CCDS4376.1, CCDS4377.1, CCDS43399.1	5q35.1	2014-09-17			ENSG00000181163	ENSG00000181163			7910	protein-coding gene	gene with protein product	"""nucleolar phosphoprotein B23"", ""numatrin"", ""nucleophosmin/nucleoplasmin family, member 1"""	164040				8471164, 8122112	Standard	NM_002520		Approved	B23, NPM	uc003mbi.3	P06748	OTTHUMG00000130465	ENST00000296930.5:c.860_863dupTCTG	5.37:g.170837544_170837547dupTCTG	ENSP00000296930:p.Trp288fs	NA	NA	NA		NA	NA	NA	170770152	NA	NA	NA	A8K3N7|B5BU00|D3DQL6|P08693|Q12826|Q13440|Q13441|Q14115|Q5EU94|Q5EU95|Q5EU96|Q5EU97|Q5EU98|Q5EU99|Q6V962|Q8WTW5|Q96AT6|Q96DC4|Q96EA5|Q9BYG9|Q9UDJ7	Frame_Shift_Ins	INS	HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain	p.W288fs	ENST00000296930.5	37	c.863_864	CCDS4376.1	5																																																																																			-	NULL		0.312	NPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NPM1	protein_coding	OTTHUMT00000252858.2	-	NM_002520		170770153	+1	no_errors	NM_002520.1	genbank	human	validated	54_36p	frame_shift_ins	INS	1.000:1.000	TCTG
PHIP	55023	genome.wustl.edu	37	6	79664636	79664637	+	Frame_Shift_Ins	INS	-	-	T	rs376189362		TCGA-AB-2967-03A-01D-0739-09	TCGA-AB-2967-11A-01D-0739-09	-	-	-	T	-	-	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	60a69167-464f-4df2-a6f9-ed402ed58f76	b5babadf-7b10-45fc-8c93-5f68a08b07ed	g.chr6:79664636_79664637insT	ENST00000275034.4	-	35	4114_4115	c.3947_3948insA	c.(3946-3948)tacfs	p.Y1316fs	PHIP_ENST00000479165.1_5'UTR	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	1316					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		CTTGAATATCGTAAGACTGGGC	0.351																																						dbGAP											0			6																																								79721356	SO:0001589	frameshift_variant	0			AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	15673	protein-coding gene	gene with protein product	"""DDB1 and CUL4 associated factor 14"""	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.3948dupA	6.37:g.79664637_79664637dupT	ENSP00000275034:p.Tyr1316fs	1645	6.48	114		16	23.81	5	79721355	578	44.26	459	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Frame_Shift_Ins	INS	HMMPfam_Bromodomain,HMMSmart_SM00297,superfamily_Bromodomain,HMMSmart_SM00320,superfamily_YVTN repeat-like/Quinoprotein amine dehydrogenase,PatternScan_BROMODOMAIN_1,PatternScan_WD_REPEATS_1,HMMPfam_WD40	p.Y1316fs	ENST00000275034.4	37	c.3948_3947	CCDS4987.1	6																																																																																			-	superfamily_Bromodomain		0.351	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PHIP	protein_coding	OTTHUMT00000041297.2	-			79721356	-1	no_errors	NM_017934.5	genbank	human	validated	54_36p	frame_shift_ins	INS	0.845:0.914	T
RAD21	5885	genome.wustl.edu	37	8	117868492	117868493	+	Frame_Shift_Ins	INS	-	-	G	rs369661655		TCGA-AB-2967-03A-01D-0739-09	TCGA-AB-2967-11A-01D-0739-09	-	-	-	G	-	-	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	60a69167-464f-4df2-a6f9-ed402ed58f76	b5babadf-7b10-45fc-8c93-5f68a08b07ed	g.chr8:117868492_117868493insG	ENST00000297338.2	-	8	1136_1137	c.849_850insC	c.(847-852)cccgttfs	p.V284fs	RAD21_ENST00000523547.1_5'Flank	NM_006265.2	NP_006256.1	O60216	RAD21_HUMAN	RAD21 homolog (S. pombe)	284					apoptotic process (GO:0006915)|chromosome segregation (GO:0007059)|DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|protein localization to chromatin (GO:0071168)|reciprocal meiotic recombination (GO:0007131)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(1)|stomach(1)	32	all_cancers(13;1.21e-21)|Lung NSC(37;0.000134)|Ovarian(258;0.0172)					ATTGGTTCAACGGGATCCACTG	0.361																																						dbGAP											0			8																																								117937674	SO:0001589	frameshift_variant	0			BC050381	CCDS6321.1	8q24.11	2014-09-17	2001-11-28		ENSG00000164754	ENSG00000164754			9811	protein-coding gene	gene with protein product	"""sister chromatid cohesion 1"""	606462	"""RAD21 (S. pombe) homolog"""			8812457	Standard	NM_006265		Approved	KIAA0078, hHR21, SCC1	uc003yod.3	O60216	OTTHUMG00000164959	ENST00000297338.2:c.850dupC	8.37:g.117868495_117868495dupG	ENSP00000297338:p.Val284fs	676	7.27	53		0	100.00	1	117937673	237	38.28	147	A8K0E0|Q15001|Q99568	Frame_Shift_Ins	INS	HMMPfam_Rad21_Rec8,HMMPfam_Rad21_Rec8_N	p.V283fs	ENST00000297338.2	37	c.850_849	CCDS6321.1	8																																																																																			-	NULL		0.361	RAD21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RAD21	protein_coding	OTTHUMT00000381184.1	-	NM_006265		117937674	-1	no_errors	NM_006265.2	genbank	human	reviewed	54_36p	frame_shift_ins	INS	1.000:0.980	G
