#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_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	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_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	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_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	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_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	i_ccds_id	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_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_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
ANKRD30BP2	149992	broad.mit.edu	37	21	14414902	14414902	+	RNA	SNP	G	G	A	rs2821609		TCGA-HT-8558-01A-21D-2395-08	TCGA-HT-8558-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39730eb2-7516-40fe-9d21-c44df7ac4c82	2c877cd5-7754-43f2-9b8e-d7179110ee18	g.chr21:14414902G>A	ENST00000507941.1	+	0	95									ankyrin repeat domain 30B pseudogene 2																		CCAGCTTGACGTCCTTGATGG	0.443																																						ENST00000507941.1																			0																																																			0							g.chr21:14414902G>A	AF427490		21q11.2	2010-06-14	2010-06-14	2010-06-14	ENSG00000224309	ENSG00000224309			16620	pseudogene	pseudogene	"""cancer/testis antigen 85"""		"""chromosome 21 open reading frame 99"""	C21orf99		12036297, 17114284	Standard	NR_026916		Approved	CT85, CTSP-1	uc002yja.4		OTTHUMG00000074164		21.37:g.14414902G>A														0	95	+									RNA	SNP	ENST00000507941.1	37																																																																																						0.443	ANKRD30BP2-004	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000372094.1	NR_026916		4	35	0	0	0	1	0	4	35				
RP11-156P1.3	0	broad.mit.edu	37	17	45128812	45128812	+	RNA	SNP	C	C	T			TCGA-HT-8558-01A-21D-2395-08	TCGA-HT-8558-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39730eb2-7516-40fe-9d21-c44df7ac4c82	2c877cd5-7754-43f2-9b8e-d7179110ee18	g.chr17:45128812C>T	ENST00000575173.1	-	0	418				LRRC37A17P_ENST00000570478.1_RNA																							AGTCCTGTTTCTGTGTGGATT	0.373																																						ENST00000575173.1																			0																																																			0							g.chr17:45128812C>T																													17.37:g.45128812C>T														0	418	-									RNA	SNP	ENST00000575173.1	37																																																																																						0.373	RP11-156P1.3-009	KNOWN	basic	lincRNA	processed_transcript	OTTHUMT00000440924.1			4	27	0	0	0	1	0	4	27				
LINC00969	440993	broad.mit.edu	37	3	195400728	195400728	+	lincRNA	SNP	A	A	G	rs12107841	byFrequency	TCGA-HT-8558-01A-21D-2395-08	TCGA-HT-8558-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39730eb2-7516-40fe-9d21-c44df7ac4c82	2c877cd5-7754-43f2-9b8e-d7179110ee18	g.chr3:195400728A>G	ENST00000445430.1	+	0	1324									long intergenic non-protein coding RNA 969																		GATTGTGCCCAGCCTGTACGC	0.587																																						ENST00000445430.1																			0																																																			0							g.chr3:195400728A>G	AK128346		3q29	2013-06-07			ENSG00000242086	ENSG00000242086		"""Long non-coding RNAs"""	48729	non-coding RNA	RNA, long non-coding							Standard	XR_427455		Approved				OTTHUMG00000155834		3.37:g.195400728A>G														0	1324	+									RNA	SNP	ENST00000445430.1	37																																																																																						0.587	LINC00969-038	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000341951.1			3	27	0	0	0	1	0	3	27				
ZNF814	730051	broad.mit.edu	37	19	58385762	58385762	+	Silent	SNP	C	C	G	rs199732634		TCGA-HT-8558-01A-21D-2395-08	TCGA-HT-8558-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39730eb2-7516-40fe-9d21-c44df7ac4c82	2c877cd5-7754-43f2-9b8e-d7179110ee18	g.chr19:58385762C>G	ENST00000435989.2	-	3	1230	c.996G>C	c.(994-996)tcG>tcC	p.S332S	ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597342.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	332					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S332S(2)		NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						ATTTGCTAAACGATTTCCCAC	0.358																																						ENST00000435989.2																			2	Substitution - coding silent(2)	p.S332S(2)	kidney(2)	NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						c.(994-996)tcG>tcC		zinc finger protein 814							25.0	25.0	25.0					19																	58385762		692	1589	2281	SO:0001819	synonymous_variant	730051				regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding	g.chr19:58385762C>G		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"""Zinc fingers, C2H2-type"", ""-"""	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.996G>C	19.37:g.58385762C>G						ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597832.1_Intron	p.S332S	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN			3	1230	-			332					A6NF35	Silent	SNP	ENST00000435989.2	37	c.996G>C	CCDS46212.1																																																																																				0.358	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		2	2	0	0	0	1	0	2	2				
EML5	161436	broad.mit.edu	37	14	89154773	89154773	+	Missense_Mutation	SNP	T	T	C	rs200233124		TCGA-HT-8558-01A-21D-2395-08	TCGA-HT-8558-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39730eb2-7516-40fe-9d21-c44df7ac4c82	2c877cd5-7754-43f2-9b8e-d7179110ee18	g.chr14:89154773T>C	ENST00000380664.5	-	18	2583	c.2584A>G	c.(2584-2586)Aaa>Gaa	p.K862E	EML5_ENST00000352093.5_Intron|EML5_ENST00000554922.1_Missense_Mutation_p.K862E			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	862						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)			breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						GTGTCATTTTTCCCCAGTGTG	0.388																																						ENST00000554922.1																			0				breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						c.(2584-2586)Aaa>Gaa		echinoderm microtubule associated protein like 5							263.0	250.0	254.0					14																	89154773		1923	4141	6064	SO:0001583	missense	161436					cytoplasm|microtubule		g.chr14:89154773T>C	AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"""WD repeat domain containing"""	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.2584A>G	14.37:g.89154773T>C	ENSP00000370039:p.Lys862Glu					EML5_ENST00000352093.5_Intron|EML5_ENST00000380664.5_Missense_Mutation_p.K862E	p.K862E	NM_183387.2	NP_899243.1	Q05BV3	EMAL5_HUMAN			18	2832	-			862					B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Missense_Mutation	SNP	ENST00000380664.5	37	c.2584A>G	CCDS45148.1	.	.	.	.	.	.	.	.	.	.	T	16.24	3.066603	0.55539	.	.	ENSG00000165521	ENST00000554922;ENST00000380664	T;T	0.47528	0.84;0.88	5.1	5.1	0.69264	Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.220980	0.31648	N	0.007287	T	0.39708	0.1088	L	0.36672	1.1	0.80722	D	1	B	0.33238	0.403	B	0.35353	0.201	T	0.19549	-1.0302	10	0.22109	T	0.4	-14.3301	14.7154	0.69265	0.0:0.0:0.0:1.0	.	862	Q05BV3	EMAL5_HUMAN	E	862	ENSP00000451998:K862E;ENSP00000370039:K862E	ENSP00000370039:K862E	K	-	1	0	EML5	88224526	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	7.525000	0.81892	2.130000	0.65690	0.533000	0.62120	AAA		0.388	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1			10	174	0	0	0	1	0	10	174				
ESPNP	284729	broad.mit.edu	37	1	17034140	17034140	+	RNA	SNP	C	C	G	rs2988286		TCGA-HT-8558-01A-21D-2395-08	TCGA-HT-8558-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39730eb2-7516-40fe-9d21-c44df7ac4c82	2c877cd5-7754-43f2-9b8e-d7179110ee18	g.chr1:17034140C>G	ENST00000492551.1	-	0	463					NR_026567.1				espin pseudogene																		GAGCACCTTGCTGTGGCCGCG	0.721																																						ENST00000492551.1																			0																																																			0							g.chr1:17034140C>G	AL035288		1p36.13	2013-05-22			ENSG00000268869	ENSG00000268869			23285	pseudogene	pseudogene						15286153	Standard	NR_026567		Approved		uc001azn.1		OTTHUMG00000000803		1.37:g.17034140C>G								NR_026567.1						0	463	-									RNA	SNP	ENST00000492551.1	37																																																																																						0.721	ESPNP-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000326311.1			2	5	0	0	0	1	0	2	5				
INTS4L1	285905	broad.mit.edu	37	7	64661070	64661070	+	RNA	SNP	G	G	A	rs62469299		TCGA-HT-8558-01A-21D-2395-08	TCGA-HT-8558-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39730eb2-7516-40fe-9d21-c44df7ac4c82	2c877cd5-7754-43f2-9b8e-d7179110ee18	g.chr7:64661070G>A	ENST00000587624.1	+	0	1371							Q96LV5	IN4L1_HUMAN	integrator complex subunit 4-like 1																		CAGCAGCAGCGAAACAGGTAA	0.512																																						ENST00000587624.1																			0																																																			0							g.chr7:64661070G>A			7q11.21	2013-03-26			ENSG00000164669	ENSG00000164669			21925	other	unknown							Standard	XR_426205		Approved	FLJ25037		Q96LV5	OTTHUMG00000156510		7.37:g.64661070G>A														0	1371	+									RNA	SNP	ENST00000587624.1	37																																																																																						0.512	INTS4L1-002	KNOWN	non_canonical_conserved|basic	processed_transcript	pseudogene	OTTHUMT00000460821.1	XR_041315		4	41	0	0	0	1	0	4	41				
MRPS9	64965	broad.mit.edu	37	2	105708997	105708997	+	Missense_Mutation	SNP	G	G	A	rs147161518	byFrequency	TCGA-HT-8558-01A-21D-2395-08	TCGA-HT-8558-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39730eb2-7516-40fe-9d21-c44df7ac4c82	2c877cd5-7754-43f2-9b8e-d7179110ee18	g.chr2:105708997G>A	ENST00000258455.3	+	8	900	c.790G>A	c.(790-792)Gag>Aag	p.E264K		NM_182640.2	NP_872578.1	P82933	RT09_HUMAN	mitochondrial ribosomal protein S9	264					DNA damage response, detection of DNA damage (GO:0042769)|peptide biosynthetic process (GO:0043043)|translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	18						ACAGTATGATGAGCAAGGAAT	0.368													G|||	6	0.00119808	0.0	0.0043	5008	,	,		17211	0.0		0.003	False		,,,				2504	0.0					ENST00000258455.3																			0				breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	18						c.(790-792)Gag>Aag		mitochondrial ribosomal protein S9		G	LYS/GLU	7,4399	12.9+/-30.5	0,7,2196	119.0	122.0	121.0		790	4.7	0.6	2	dbSNP_134	121	54,8546	34.3+/-88.2	0,54,4246	yes	missense	MRPS9	NM_182640.2	56	0,61,6442	AA,AG,GG		0.6279,0.1589,0.469	possibly-damaging	264/397	105708997	61,12945	2203	4300	6503	SO:0001583	missense	64965				DNA damage response, detection of DNA damage|translation	mitochondrial small ribosomal subunit	protein binding|structural constituent of ribosome	g.chr2:105708997G>A		CCDS2065.1	2q12.1	2012-09-13			ENSG00000135972	ENSG00000135972		"""Mitochondrial ribosomal proteins / small subunits"""	14501	protein-coding gene	gene with protein product	"""28S ribosomal protein S9, mitochondrial"""	611975				11279123	Standard	NM_182640		Approved	RPMS9, MRP-S9, S9mt	uc002tcn.4	P82933	OTTHUMG00000130807	ENST00000258455.3:c.790G>A	2.37:g.105708997G>A	ENSP00000258455:p.Glu264Lys						p.E264K	NM_182640.2	NP_872578.1	P82933	RT09_HUMAN			8	900	+			264					Q6PG40	Missense_Mutation	SNP	ENST00000258455.3	37	c.790G>A	CCDS2065.1	6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	15.27	2.783817	0.49891	0.001589	0.006279	ENSG00000135972	ENST00000258455	D	0.92348	-3.02	5.61	4.71	0.59529	.	0.359615	0.33438	N	0.004916	D	0.86239	0.5885	L	0.52364	1.645	0.46044	D	0.998836	P	0.36990	0.577	B	0.33568	0.166	D	0.87090	0.2172	10	0.49607	T	0.09	-27.1935	16.6325	0.85037	0.0:0.1301:0.8699:0.0	.	264	P82933	RT09_HUMAN	K	264	ENSP00000258455:E264K	ENSP00000258455:E264K	E	+	1	0	MRPS9	105075429	1.000000	0.71417	0.619000	0.29118	0.989000	0.77384	4.529000	0.60588	1.459000	0.47892	0.655000	0.94253	GAG		0.368	MRPS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253352.1	NM_182640		4	62	0	0	0	1	0	4	62				
ZNF682	91120	broad.mit.edu	37	19	20117231	20117231	+	Missense_Mutation	SNP	C	C	G	rs199794786		TCGA-HT-8558-01A-21D-2395-08	TCGA-HT-8558-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39730eb2-7516-40fe-9d21-c44df7ac4c82	2c877cd5-7754-43f2-9b8e-d7179110ee18	g.chr19:20117231C>G	ENST00000397165.2	-	4	1240	c.1080G>C	c.(1078-1080)aaG>aaC	p.K360N	ZNF682_ENST00000358523.5_Missense_Mutation_p.K328N|ZNF682_ENST00000397162.1_Missense_Mutation_p.K328N|ZNF682_ENST00000596019.1_Intron|ZNF682_ENST00000597972.1_Missense_Mutation_p.K366N|ZNF682_ENST00000595736.1_Missense_Mutation_p.K284N	NM_033196.2	NP_149973.1	O95780	ZN682_HUMAN	zinc finger protein 682	360					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	14						TATGAATTACCTTATGTTCAG	0.363																																						ENST00000397165.2																			0				endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	14						c.(1078-1080)aaG>aaC		zinc finger protein 682							51.0	55.0	53.0					19																	20117231		2112	4255	6367	SO:0001583	missense	91120				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:20117231C>G	AC006539	CCDS42533.1, CCDS42534.1	19p12	2014-02-13			ENSG00000197124	ENSG00000197124		"""Zinc fingers, C2H2-type"", ""-"""	28857	protein-coding gene	gene with protein product							Standard	NM_033196		Approved	BC39498_3	uc002noq.3	O95780	OTTHUMG00000182650	ENST00000397165.2:c.1080G>C	19.37:g.20117231C>G	ENSP00000380351:p.Lys360Asn					ZNF682_ENST00000397162.1_Missense_Mutation_p.K328N|ZNF682_ENST00000358523.5_Missense_Mutation_p.K328N|ZNF682_ENST00000597972.1_Missense_Mutation_p.K366N|ZNF682_ENST00000595736.1_Missense_Mutation_p.K284N|ZNF682_ENST00000596019.1_Intron	p.K360N	NM_033196.2	NP_149973.1	O95780	ZN682_HUMAN			4	1240	-			360					B3KU64|E9PFJ5|Q96JV9	Missense_Mutation	SNP	ENST00000397165.2	37	c.1080G>C	CCDS42533.1	.	.	.	.	.	.	.	.	.	.	C	12.83	2.055901	0.36277	.	.	ENSG00000197124	ENST00000397165;ENST00000397162;ENST00000341262;ENST00000358523	T;T;T	0.18657	2.2;2.2;2.2	1.09	-0.0727	0.13738	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.26882	0.0658	L	0.58669	1.825	0.23758	N	0.996921	P	0.40909	0.732	P	0.48952	0.596	T	0.21518	-1.0243	9	0.87932	D	0	.	4.8624	0.13590	0.0:0.7293:0.0:0.2707	.	360	O95780	ZN682_HUMAN	N	360;328;29;328	ENSP00000380351:K360N;ENSP00000380348:K328N;ENSP00000351324:K328N	ENSP00000340236:K29N	K	-	3	2	ZNF682	19978231	0.000000	0.05858	0.065000	0.19835	0.061000	0.15899	-0.304000	0.08199	0.488000	0.27723	0.491000	0.48974	AAG		0.363	ZNF682-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462888.1	NM_033196		5	37	0	0	0	1	0	5	37				
RP11-156P1.3	0	broad.mit.edu	37	17	45128792	45128792	+	RNA	SNP	G	G	T			TCGA-HT-8558-01A-21D-2395-08	TCGA-HT-8558-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39730eb2-7516-40fe-9d21-c44df7ac4c82	2c877cd5-7754-43f2-9b8e-d7179110ee18	g.chr17:45128792G>T	ENST00000575173.1	-	0	418				LRRC37A17P_ENST00000570478.1_RNA																							AATTCAGGTTGTCAGAATGCA	0.373																																						ENST00000575173.1																			0																																																			0							g.chr17:45128792G>T																													17.37:g.45128792G>T														0	418	-									RNA	SNP	ENST00000575173.1	37																																																																																						0.373	RP11-156P1.3-009	KNOWN	basic	lincRNA	processed_transcript	OTTHUMT00000440924.1			4	21	1	0	0.150653	1	0.158186	4	21				
C7orf55-LUC7L2	100996928	broad.mit.edu	37	7	139094365	139094366	+	Frame_Shift_Del	DEL	AG	AG	-	rs368249579	byFrequency	TCGA-HT-8558-01A-21D-2395-08	TCGA-HT-8558-10A-01D-2396-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	39730eb2-7516-40fe-9d21-c44df7ac4c82	2c877cd5-7754-43f2-9b8e-d7179110ee18	g.chr7:139094365_139094366delAG	ENST00000354926.4	+	7	1098_1099	c.744_745delAG	c.(742-747)gaagagfs	p.EE248fs	LUC7L2_ENST00000541515.3_Frame_Shift_Del_p.EE314fs|C7orf55-LUC7L2_ENST00000263545.6_Frame_Shift_Del_p.EE247fs|C7orf55-LUC7L2_ENST00000541170.3_Frame_Shift_Del_p.EE245fs	NM_001270643.1|NM_016019.4	NP_001257572.1|NP_057103.2			C7orf55-LUC7L2 readthrough																		AACGAAGAGAAGAGAGAGAGAG	0.391														64	0.0127796	0.028	0.0014	5008	,	,		16418	0.004		0.002	False		,,,				2504	0.0204					ENST00000354926.4																			0											c.(742-747)gaagfs						136,3410		1,134,1638						5.1	1.0			34	290,7544		0,290,3627	no	frameshift	LUC7L2	NM_016019.3		1,424,5265	A1A1,A1R,RR		3.7018,3.8353,3.7434				426,10954				SO:0001589	frameshift_variant	0							g.chr7:139094365_139094366delAG		CCDS59084.1	7q34	2013-02-14			ENSG00000146963	ENSG00000146963			44671	other	readthrough							Standard	NM_001244584		Approved		uc011kqt.3		OTTHUMG00000151717	ENST00000354926.4:c.744_745delAG	7.37:g.139094375_139094376delAG	ENSP00000347005:p.Glu248fs					LUC7L2_ENST00000541515.3_Frame_Shift_Del_p.EE314fs|C7orf55-LUC7L2_ENST00000541170.3_Frame_Shift_Del_p.EE245fs|C7orf55-LUC7L2_ENST00000263545.6_Frame_Shift_Del_p.EE247fs	p.EE248fs	NM_016019.3	NP_057103.2					7	1098_1099	+									Frame_Shift_Del	DEL	ENST00000354926.4	37	c.744_745delAG	CCDS43656.1																																																																																				0.391	C7orf55-LUC7L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323618.2			4	9						4	9	---	---	---	---
