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2014.12.11.blog_spotlight_variants_snpeff.vcf
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##fileformat=VCFv4.1
##fileDate=2014/06/17
##source=Manual_Curation_By_Andrew_Jesaitis
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##SnpEffVersion="4.0e (build 2014-09-13), by Pablo Cingolani"
##SnpEffCmd="SnpEff GRCh37.75 -hgvs -o vcf /Users/andrewjesaitis/Desktop/blog_spotlight_variants.vcf "
##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank | Genotype_Number [ | ERRORS | WARNINGS ] )' ">
##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' ">
##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' ">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE
7 117120154 . A AT . . EFF=frameshift_variant+stop_gained(HIGH||agg/Tagg|p.Arg3_Ser4fs/c.7_8insT|1480|CFTR|protein_coding|CODING|ENST00000003084|1|1),frameshift_variant+stop_gained(HIGH||agg/Tagg|p.Arg3_Ser4fs/c.7_8insT|1419|CFTR|protein_coding|CODING|ENST00000454343|1|1),frameshift_variant+stop_gained(HIGH||agg/Tagg|p.Arg3_Ser4fs/c.7_8insT|1437|CFTR|protein_coding|CODING|ENST00000426809|1|1|WARNING_TRANSCRIPT_INCOMPLETE),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.7_8insT|1419|CFTR|protein_coding|CODING|ENST00000454343|1|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.7_8insT|1419|CFTR|protein_coding|CODING|ENST00000454343|3|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.7_8insT|1419|CFTR|protein_coding|CODING|ENST00000454343|2|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.7_8insT|1480|CFTR|protein_coding|CODING|ENST00000003084|1|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.7_8insT|1480|CFTR|protein_coding|CODING|ENST00000003084|3|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.7_8insT|1480|CFTR|protein_coding|CODING|ENST00000003084|2|1),intron_variant(MODIFIER|||n.166+4293_166+4294insT||CFTR|processed_transcript|CODING|ENST00000546407|2|1),intron_variant(MODIFIER|||c.-191+407_-191+408insT|35|CFTR|protein_coding|CODING|ENST00000446805|2|1|WARNING_TRANSCRIPT_INCOMPLETE) GT 0/1
7 117105835 . TTTT T . . EFF=upstream_gene_variant(MODIFIER||2|||CFTR|processed_transcript|CODING|ENST00000546407||1),intergenic_region(MODIFIER||||||||||1),non_coding_exon_variant(MODIFIER|||||CFTR|processed_transcript|CODING|ENST00000546407|1|1) GT 0/1
7 117307159 . TT T . . EFF=frameshift_variant+stop_lost(HIGH||tag/|p.Ter1481fs/c.4441delT|1480|CFTR|protein_coding|CODING|ENST00000003084|27|1),frameshift_variant+stop_lost(HIGH||tag/|p.Ter1420fs/c.4258delT|1419|CFTR|protein_coding|CODING|ENST00000454343|26|1),downstream_gene_variant(MODIFIER||35||1437|CFTR|protein_coding|CODING|ENST00000426809||1|WARNING_TRANSCRIPT_INCOMPLETE),intron_variant(MODIFIER|||c.366+1542delT|155|CFTR|protein_coding|CODING|ENST00000600166|3|1|WARNING_TRANSCRIPT_NO_START_CODON) GT 0/1
7 117119513 . C CA . . EFF=splice_acceptor_variant(HIGH|||c.1_2insA|35|CFTR|protein_coding|CODING|ENST00000446805|2|1|WARNING_TRANSCRIPT_INCOMPLETE),upstream_gene_variant(MODIFIER||503||1480|CFTR|protein_coding|CODING|ENST00000003084||1),upstream_gene_variant(MODIFIER||503||1419|CFTR|protein_coding|CODING|ENST00000454343||1),upstream_gene_variant(MODIFIER||635||1437|CFTR|protein_coding|CODING|ENST00000426809||1|WARNING_TRANSCRIPT_INCOMPLETE),intron_variant(MODIFIER|||n.166+3652_166+3653insA||CFTR|processed_transcript|CODING|ENST00000546407|2|1),intron_variant(MODIFIER|||c.-423-2_-423-1insA|35|CFTR|protein_coding|CODING|ENST00000446805|1|1|WARNING_TRANSCRIPT_INCOMPLETE);LOF=(CFTR|ENSG00000001626|11|0.09) GT 0/1
7 117144417 . G GATG . . EFF=splice_donor_variant(HIGH|||c.1_2insATG|35|CFTR|protein_coding|CODING|ENST00000446805|3|1|WARNING_TRANSCRIPT_INCOMPLETE),splice_donor_variant(HIGH|||c.165_166insATG|1437|CFTR|protein_coding|CODING|ENST00000426809|2|1|WARNING_TRANSCRIPT_INCOMPLETE),splice_donor_variant(HIGH|||c.165_166insATG|1480|CFTR|protein_coding|CODING|ENST00000003084|2|1),splice_donor_variant(HIGH|||c.165_166insATG|1419|CFTR|protein_coding|CODING|ENST00000454343|2|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.165_166insATG|1419|CFTR|protein_coding|CODING|ENST00000454343|1|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.165_166insATG|1419|CFTR|protein_coding|CODING|ENST00000454343|3|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.165_166insATG|1419|CFTR|protein_coding|CODING|ENST00000454343|2|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.165_166insATG|1480|CFTR|protein_coding|CODING|ENST00000003084|1|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.165_166insATG|1480|CFTR|protein_coding|CODING|ENST00000003084|3|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.165_166insATG|1480|CFTR|protein_coding|CODING|ENST00000003084|2|1),downstream_gene_variant(MODIFIER||56|||CFTR|processed_transcript|CODING|ENST00000546407||1),intron_variant(MODIFIER|||c.164+1_164+2insATG|1480|CFTR|protein_coding|CODING|ENST00000003084|2|1),intron_variant(MODIFIER|||c.164+1_164+2insATG|1437|CFTR|protein_coding|CODING|ENST00000426809|2|1|WARNING_TRANSCRIPT_INCOMPLETE),intron_variant(MODIFIER|||c.-80+1_-80+2insATG|35|CFTR|protein_coding|CODING|ENST00000446805|3|1|WARNING_TRANSCRIPT_INCOMPLETE),intron_variant(MODIFIER|||c.164+1_164+2insATG|1419|CFTR|protein_coding|CODING|ENST00000454343|2|1);LOF=(CFTR|ENSG00000001626|11|0.36) GT 0/1
7 117307123 . AGAG A . . EFF=frameshift_variant(HIGH||ga/|p.???1439fs/c.4315_4317delGAG|1437|CFTR|protein_coding|CODING|ENST00000426809|26|1|WARNING_TRANSCRIPT_INCOMPLETE),inframe_deletion(MODERATE||gag/|p.Glu1469del/c.4405_4407delGAG|1480|CFTR|protein_coding|CODING|ENST00000003084|27|1),inframe_deletion(MODERATE||gag/|p.Glu1408del/c.4222_4224delGAG|1419|CFTR|protein_coding|CODING|ENST00000454343|26|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.4222_4224delGAG|1419|CFTR|protein_coding|CODING|ENST00000454343|25|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.4222_4224delGAG|1419|CFTR|protein_coding|CODING|ENST00000454343|21|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.4222_4224delGAG|1419|CFTR|protein_coding|CODING|ENST00000454343|22|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.4222_4224delGAG|1419|CFTR|protein_coding|CODING|ENST00000454343|24|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.4222_4224delGAG|1419|CFTR|protein_coding|CODING|ENST00000454343|23|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.4222_4224delGAG|1419|CFTR|protein_coding|CODING|ENST00000454343|20|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.4222_4224delGAG|1419|CFTR|protein_coding|CODING|ENST00000454343|26|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.4405_4407delGAG|1480|CFTR|protein_coding|CODING|ENST00000003084|26|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.4405_4407delGAG|1480|CFTR|protein_coding|CODING|ENST00000003084|22|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.4405_4407delGAG|1480|CFTR|protein_coding|CODING|ENST00000003084|23|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.4405_4407delGAG|1480|CFTR|protein_coding|CODING|ENST00000003084|25|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.4405_4407delGAG|1480|CFTR|protein_coding|CODING|ENST00000003084|24|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.4405_4407delGAG|1480|CFTR|protein_coding|CODING|ENST00000003084|21|1),sequence_feature[topological_domain:Cytoplasmic](LOW|||c.4405_4407delGAG|1480|CFTR|protein_coding|CODING|ENST00000003084|27|1),downstream_gene_variant(MODIFIER||0|c.4315_4317delGAG|1437|CFTR|protein_coding|CODING|ENST00000426809||1|WARNING_TRANSCRIPT_INCOMPLETE),intron_variant(MODIFIER|||c.366+1506_366+1508delGAG|155|CFTR|protein_coding|CODING|ENST00000600166|3|1|WARNING_TRANSCRIPT_NO_START_CODON) GT 0/1