#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
NCOA6	23054	broad.mit.edu	37	20	33345744	33345744	+	Silent	SNP	C	C	T			TCGA-E8-A416-01A-11D-A23M-08	TCGA-E8-A416-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c8381701-31cb-465a-bdf2-1b8132be7a14	d60fc127-2b47-4ce1-a120-f43adc2ae776	g.chr20:33345744C>T	ENST00000374796.2	-	8	3377	c.807G>A	c.(805-807)caG>caA	p.Q269Q	NCOA6_ENST00000359003.2_Silent_p.Q269Q			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	269	CREBBP-binding region.|Gln-rich.|NCOA1-binding region.|TBP/GTF2A-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.Q269Q(15)		NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						gctgctgctgctgttgttgtt	0.537																																						ENST00000374796.2																			15	Substitution - coding silent(15)	p.Q269Q(15)	lung(5)|prostate(4)|endometrium(3)|central_nervous_system(1)|urinary_tract(1)|kidney(1)	NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						c.(805-807)caG>caA		nuclear receptor coactivator 6							64.0	52.0	56.0					20																	33345744		2203	4300	6503	SO:0001819	synonymous_variant	23054				brain development|cellular lipid metabolic process|DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|heart development|myeloid cell differentiation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|transcription initiation from RNA polymerase II promoter	transcription factor complex	chromatin binding|enzyme binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|retinoid X receptor binding|thyroid hormone receptor binding	g.chr20:33345744C>T	AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"""nuclear receptor coactivator RAP250"", ""activating signal cointegrator-2"", ""peroxisome proliferator-activated receptor interacting protein"""	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.807G>A	20.37:g.33345744C>T						NCOA6_ENST00000359003.2_Silent_p.Q269Q	p.Q269Q			Q14686	NCOA6_HUMAN			8	3377	-			269			CREBBP-binding region.|Gln-rich.|NCOA1-binding region.|TBP/GTF2A-binding region.		A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Silent	SNP	ENST00000374796.2	37	c.807G>A	CCDS13241.1																																																																																				0.537	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		4	41	0	0	0	1	0	4	41				
ANKRD30B	374860	broad.mit.edu	37	18	14752601	14752601	+	Silent	SNP	A	A	G	rs200428778	byFrequency	TCGA-E8-A416-01A-11D-A23M-08	TCGA-E8-A416-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c8381701-31cb-465a-bdf2-1b8132be7a14	d60fc127-2b47-4ce1-a120-f43adc2ae776	g.chr18:14752601A>G	ENST00000358984.4	+	2	438	c.258A>G	c.(256-258)gcA>gcG	p.A86A	ANKRD30B_ENST00000447268.2_Silent_p.A86A|ANKRD30B_ENST00000579292.1_Intron	NM_001145029.1	NP_001138501.1	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B	86										breast(3)|endometrium(4)|kidney(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	22						ATGGCCATGCAGAAGTAGTAA	0.448													a|||	12	0.00239617	0.0008	0.0	5008	,	,		17952	0.0		0.0099	False		,,,				2504	0.001					ENST00000358984.4																			0				breast(3)|endometrium(4)|kidney(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	22						c.(256-258)gcA>gcG		ankyrin repeat domain 30B		A		1,1383		0,1,691	69.0	61.0	64.0		258	-3.2	0.0	18		64	16,3166		0,16,1575	no	coding-synonymous	ANKRD30B	NM_001145029.1		0,17,2266	GG,GA,AA		0.5028,0.0723,0.3723		86/1393	14752601	17,4549	692	1591	2283	SO:0001819	synonymous_variant	374860							g.chr18:14752601A>G	BC028407	CCDS54182.1	18p11.21	2013-01-10			ENSG00000180777	ENSG00000180777		"""Ankyrin repeat domain containing"""	24165	protein-coding gene	gene with protein product						11280766	Standard	NM_001145029		Approved	NY-BR-1.1	uc010dlo.2	Q9BXX2		ENST00000358984.4:c.258A>G	18.37:g.14752601A>G						ANKRD30B_ENST00000579292.1_Intron|ANKRD30B_ENST00000447268.2_Silent_p.A86A	p.A86A	NM_001145029.1	NP_001138501.1	Q9BXX2	AN30B_HUMAN			2	438	+			86					B4DGP1|F8WAG3|Q4G175	Silent	SNP	ENST00000358984.4	37	c.258A>G	CCDS54182.1																																																																																				0.448	ANKRD30B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443557.1	NM_001145029		3	26	0	0	0	1	0	3	26				
CDCA7	83879	broad.mit.edu	37	2	174223463	174223463	+	Silent	SNP	G	G	A	rs139753635	byFrequency	TCGA-E8-A416-01A-11D-A23M-08	TCGA-E8-A416-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c8381701-31cb-465a-bdf2-1b8132be7a14	d60fc127-2b47-4ce1-a120-f43adc2ae776	g.chr2:174223463G>A	ENST00000347703.3	+	2	189	c.45G>A	c.(43-45)aaG>aaA	p.K15K	CDCA7_ENST00000392567.2_Silent_p.K15K|CDCA7_ENST00000410019.3_Intron|CDCA7_ENST00000306721.3_Silent_p.K15K|AC092573.2_ENST00000437243.1_RNA|CDCA7_ENST00000410101.3_Silent_p.K15K	NM_145810.2	NP_665809.1	Q9BWT1	CDCA7_HUMAN	cell division cycle associated 7	15					apoptotic process (GO:0006915)|regulation of cell proliferation (GO:0042127)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)	18			OV - Ovarian serous cystadenocarcinoma(117;0.116)			GAGTAAAGAAGAACTTAAAGA	0.328													G|||	3	0.000599042	0.0	0.0029	5008	,	,		19665	0.0		0.001	False		,,,				2504	0.0					ENST00000306721.3																			0				breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)	18						c.(43-45)aaG>aaA		cell division cycle associated 7		G	,	1,4405	2.1+/-5.4	0,1,2202	76.0	81.0	80.0		45,45	4.9	1.0	2	dbSNP_134	80	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous,coding-synonymous	CDCA7	NM_031942.4,NM_145810.2	,	0,12,6491	AA,AG,GG		0.1279,0.0227,0.0923	,	15/451,15/372	174223463	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	83879				regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus		g.chr2:174223463G>A	BG354580	CCDS2252.1, CCDS2253.1	2q31.1	2008-02-05			ENSG00000144354	ENSG00000144354			14628	protein-coding gene	gene with protein product		609937				11598121, 12188893	Standard	NM_145810		Approved	FLJ14736, JPO1	uc002uic.1	Q9BWT1	OTTHUMG00000132296	ENST00000347703.3:c.45G>A	2.37:g.174223463G>A						CDCA7_ENST00000392567.2_Silent_p.K15K|CDCA7_ENST00000347703.3_Silent_p.K15K|CDCA7_ENST00000410101.3_Silent_p.K15K|CDCA7_ENST00000410019.3_Intron	p.K15K	NM_031942.4	NP_114148.3	Q9BWT1	CDCA7_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.116)		2	148	+			0					B4DLP8|B4DV66|Q53EW5|Q580W9|Q658K4|Q658N4|Q8NBY9|Q96BV8|Q96SP5	Silent	SNP	ENST00000347703.3	37	c.45G>A	CCDS2253.1																																																																																				0.328	CDCA7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255400.1	NM_031942		4	58	0	0	0	1	0	4	58				
LOC494141	494141	broad.mit.edu	37	11	18231289	18231289	+	Missense_Mutation	SNP	C	C	A	rs4757627	byFrequency	TCGA-E8-A416-01A-11D-A23M-08	TCGA-E8-A416-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c8381701-31cb-465a-bdf2-1b8132be7a14	d60fc127-2b47-4ce1-a120-f43adc2ae776	g.chr11:18231289C>A	ENST00000527059.1	+	1	535	c.75C>A	c.(73-75)ttC>ttA	p.F25L	RP11-113D6.10_ENST00000534640.1_Missense_Mutation_p.F25L|RP11-113D6.10_ENST00000340135.3_Missense_Mutation_p.F25L																							CTAACATCTTCGAAACAAGAT	0.363													C|||	1302	0.259984	0.1762	0.304	5008	,	,		21797	0.0456		0.4881	False		,,,				2504	0.3282					ENST00000527059.1																			0											c.(73-75)ttC>ttA																																						SO:0001583	missense	0							g.chr11:18231289C>A																												ENST00000527059.1:c.75C>A	11.37:g.18231289C>A	ENSP00000436511:p.Phe25Leu					RP11-113D6.10_ENST00000340135.3_Missense_Mutation_p.F25L|RP11-113D6.10_ENST00000534640.1_Missense_Mutation_p.F25L	p.F25L							1	535	+									Missense_Mutation	SNP	ENST00000527059.1	37	c.75C>A		592	0.27106227106227104	89	0.18089430894308944	116	0.32044198895027626	13	0.022727272727272728	374	0.49340369393139843	C	8.834	0.940531	0.18281	.	.	ENSG00000189332	ENST00000340135;ENST00000534640;ENST00000527059	T;T;T	0.71817	-0.6;-0.6;-0.6	0.742	0.742	0.18341	.	1.286270	0.05338	N	0.529645	T	0.00012	0.0000	.	.	.	.	.	.	.	.	.	.	.	.	T	0.31138	-0.9954	6	0.10902	T	0.67	.	7.2708	0.26256	0.0:1.0:0.0:0.0	rs4757627;rs4757627	.	.	.	L	25	ENSP00000342780:F25L;ENSP00000437119:F25L;ENSP00000436511:F25L	ENSP00000342780:F25L	F	+	3	2	RP11-113D6.10	18187865	0.970000	0.33590	0.002000	0.10522	0.016000	0.09150	2.541000	0.45735	0.654000	0.30846	0.305000	0.20034	TTC		0.363	RP11-113D6.10-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000389801.2			6	52	1	0	0.0215528	1	0.0215528	6	52				
MICAL1	64780	broad.mit.edu	37	6	109767929	109767929	+	Silent	SNP	C	C	T	rs41288556|rs552227069|rs35260632	byFrequency	TCGA-E8-A416-01A-11D-A23M-08	TCGA-E8-A416-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c8381701-31cb-465a-bdf2-1b8132be7a14	d60fc127-2b47-4ce1-a120-f43adc2ae776	g.chr6:109767929C>T	ENST00000358807.3	-	18	2585	c.2274G>A	c.(2272-2274)gcG>gcA	p.A758A	MICAL1_ENST00000368952.4_Silent_p.A777A|MICAL1_ENST00000358577.3_Silent_p.A672A	NM_022765.3	NP_073602.3	Q8TDZ2	MICA1_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 1	758			A -> E (in dbSNP:rs9320288).|A -> K (requires 2 nucleotide substitutions; dbSNP:rs35260632). {ECO:0000269|PubMed:11827972, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.|A -> S (in dbSNP:rs59056467).|A -> T (in dbSNP:rs59056467).		actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of protein phosphorylation (GO:0001933)|oxidation-reduction process (GO:0055114)|signal transduction (GO:0007165)|sulfur oxidation (GO:0019417)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|liver(1)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	40		all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149)		Epithelial(106;0.0142)|all cancers(137;0.0197)|OV - Ovarian serous cystadenocarcinoma(136;0.0233)|BRCA - Breast invasive adenocarcinoma(108;0.0574)		CGCTGCCTTCCGCTTTGTGGT	0.572													C|||	23	0.00459265	0.0	0.0072	5008	,	,		18546	0.0		0.0109	False		,,,				2504	0.0072					ENST00000368952.4																			0				NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|liver(1)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	40						c.(2329-2331)gcG>gcA		microtubule associated monooxygenase, calponin and LIM domain containing 1		C	,	7,4399	12.9+/-30.5	0,7,2196	78.0	69.0	72.0		2016,2274	-2.7	0.0	6	dbSNP_127	72	116,8484	59.1+/-120.7	2,112,4186	no	coding-synonymous,coding-synonymous	MICAL1	NM_001159291.1,NM_022765.3	,	2,119,6382	TT,TC,CC		1.3488,0.1589,0.9457	,	672/982,758/1068	109767929	123,12883	2203	4300	6503	SO:0001819	synonymous_variant	64780				cytoskeleton organization|signal transduction	cytoplasm|intermediate filament	SH3 domain binding|zinc ion binding	g.chr6:109767929C>T	AB048948	CCDS5076.1, CCDS55047.1	6q21	2013-03-26	2013-03-26	2005-02-16	ENSG00000135596	ENSG00000135596			20619	protein-coding gene	gene with protein product		607129	"""NEDD9 interacting protein with calponin homology and LIM domains"""	NICAL		11827972	Standard	NM_022765		Approved	MICAL, FLJ11937, DKFZp434B1517, FLJ21739	uc003ptk.3	Q8TDZ2	OTTHUMG00000015350	ENST00000358807.3:c.2274G>A	6.37:g.109767929C>T						MICAL1_ENST00000358577.3_Silent_p.A672A|MICAL1_ENST00000358807.3_Silent_p.A758A	p.A777A			Q8TDZ2	MICA1_HUMAN		Epithelial(106;0.0142)|all cancers(137;0.0197)|OV - Ovarian serous cystadenocarcinoma(136;0.0233)|BRCA - Breast invasive adenocarcinoma(108;0.0574)	18	2621	-		all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149)	758					B7Z3R5|E1P5F0|Q7Z633|Q8IVS9|Q96G47|Q9H6X6|Q9H7I0|Q9HAA1|Q9UFF7	Silent	SNP	ENST00000358807.3	37	c.2331G>A	CCDS5076.1																																																																																				0.572	MICAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041759.2	NM_022765		3	21	0	0	0	1	0	3	21				
RP11-404F10.2	0	broad.mit.edu	37	1	160640798	160640798	+	RNA	DEL	T	T	-			TCGA-E8-A416-01A-11D-A23M-08	TCGA-E8-A416-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c8381701-31cb-465a-bdf2-1b8132be7a14	d60fc127-2b47-4ce1-a120-f43adc2ae776	g.chr1:160640798delT	ENST00000443928.2	+	0	0				RP11-404F10.2_ENST00000598917.2_RNA|RP11-404F10.2_ENST00000588034.1_RNA																							TTCTGAACAATTTTTTTTTTA	0.428																																						ENST00000598917.1																			0																																																			0							g.chr1:160640798delT																													1.37:g.160640798delT														0	231	+									RNA	DEL	ENST00000443928.2	37																																																																																						0.428	RP11-404F10.2-001	KNOWN	basic|exp_conf	antisense	antisense	OTTHUMT00000060453.3			2	4						2	4	---	---	---	---
DDX52	11056	broad.mit.edu	37	17	36003613	36003614	+	5'Flank	INS	-	-	T	rs59697282|rs377450634		TCGA-E8-A416-01A-11D-A23M-08	TCGA-E8-A416-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c8381701-31cb-465a-bdf2-1b8132be7a14	d60fc127-2b47-4ce1-a120-f43adc2ae776	g.chr17:36003613_36003614insT	ENST00000349699.2	-	0	0				RP11-697E22.2_ENST00000586163.1_RNA|DDX52_ENST00000394367.3_5'Flank|RP11-697E22.2_ENST00000586950.1_RNA	NM_007010.3	NP_008941.2	Q9Y2R4	DDX52_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 52							membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(5)|ovary(1)|skin(3)	17		Breast(25;0.00637)|Ovarian(249;0.15)				CATTAtttatcttttttttttt	0.51																																						ENST00000586163.1																			0																																																	SO:0001631	upstream_gene_variant	0							g.chr17:36003613_36003614insT	AF077033	CCDS11323.1	17q21.1	2014-05-06			ENSG00000141141	ENSG00000278053		"""DEAD-boxes"""	20038	protein-coding gene	gene with protein product		612500				11124703	Standard	XM_006721650		Approved	ROK1	uc002hoi.2	Q9Y2R4	OTTHUMG00000188475		17.37:g.36003624_36003624dupT	Exception_encountered					RP11-697E22.2_ENST00000586950.1_RNA								0	590	+								Q86YG1|Q8N213|Q9NVE0|Q9Y482	RNA	INS	ENST00000349699.2	37		CCDS11323.1																																																																																				0.510	DDX52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256795.1	NM_152300		2	4						2	4	---	---	---	---
