##fileformat=VCFv4.1
##VEP="v98" time="2019-10-09 14:03:13" cache="/nfs/public/release/ensweb-data/latest/tools/www/e98/vep/cache/homo_sapiens/98_GRCh38" db="homo_sapiens_core_98_38@hh-mysql-ens-species-web-1" 1000genomes="phase3" COSMIC="89" ClinVar="201907" ESP="V2-SSA137" HGMD-PUBLIC="20184" assembly="GRCh38.p13" dbSNP="152" gencode="GENCODE 32" genebuild="2014-07" gnomAD="r2.1" polyphen="2.2.2" regbuild="1.0" sift="sift5.2.2"
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID|MANE|TSL|APPRIS|SIFT|PolyPhen|AF|CLIN_SIG|SOMATIC|PHENO|PUBMED|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
1	65568	1_65568_A/G	A	G	.	.	CSQ=G|upstream_gene_variant|MODIFIER|OR4F5|ENSG00000186092|Transcript|ENST00000335137.4|protein_coding|||||||||||3487|1||HGNC|HGNC:14825|||P1|||||||||||,G|downstream_gene_variant|MODIFIER|OR4G11P|ENSG00000240361|Transcript|ENST00000492842.2|transcribed_unprocessed_pseudogene|||||||||||1681|1||HGNC|HGNC:31276||||||||||||||,G|missense_variant|MODERATE|OR4F5|ENSG00000186092|Transcript|ENST00000641515.2|protein_coding|2/3||||64|4|2|K/E|Aag/Gag|||1||HGNC|HGNC:14825||||tolerated_low_confidence(0.33)|benign(0.007)|||||||||,G|downstream_gene_variant|MODIFIER|OR4G11P|ENSG00000240361|Transcript|ENST00000642116.1|lncRNA|||||||||||1452|1||HGNC|HGNC:31276||||||||||||||
3	319781	3_319781_A/G	A	G	.	.	CSQ=G|missense_variant|MODERATE|CHL1|ENSG00000134121|Transcript|ENST00000256509.7|protein_coding|3/28||||480|5|2|E/G|gAg/gGg|rs1247101959||1||HGNC|HGNC:1939|NM_006614.4|1|P3|deleterious_low_confidence(0.02)|benign(0.037)|||||||||,G|missense_variant|MODERATE|CHL1|ENSG00000134121|Transcript|ENST00000397491.6|protein_coding|3/27||||472|5|2|E/G|gAg/gGg|rs1247101959||1||HGNC|HGNC:1939||1|A2|deleterious_low_confidence(0.02)|benign(0.024)|||||||||,G|missense_variant|MODERATE|CHL1|ENSG00000134121|Transcript|ENST00000421198.5|protein_coding|3/5||||258|5|2|E/G|gAg/gGg|rs1247101959||1|cds_end_NF|HGNC|HGNC:1939||4||deleterious(0.02)|benign(0.024)|||||||||,G|missense_variant|MODERATE|CHL1|ENSG00000134121|Transcript|ENST00000427688.5|protein_coding|2/3||||380|5|2|E/G|gAg/gGg|rs1247101959||1|cds_end_NF|HGNC|HGNC:1939||4||deleterious(0.01)|benign(0.024)|||||||||,G|missense_variant|MODERATE|CHL1|ENSG00000134121|Transcript|ENST00000435603.5|protein_coding|2/6||||185|5|2|E/G|gAg/gGg|rs1247101959||1|cds_end_NF|HGNC|HGNC:1939||5||deleterious_low_confidence(0.01)|benign(0.024)|||||||||,G|missense_variant|MODERATE|CHL1|ENSG00000134121|Transcript|ENST00000449294.6|protein_coding|3/5||||345|5|2|E/G|gAg/gGg|rs1247101959||1|cds_end_NF|HGNC|HGNC:1939||4||deleterious(0.02)|benign(0.024)|||||||||,G|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|CHL1|ENSG00000134121|Transcript|ENST00000453040.5|nonsense_mediated_decay|3/25||||628|||||rs1247101959||1||HGNC|HGNC:1939||2||||||||||||,G|upstream_gene_variant|MODIFIER|CHL1|ENSG00000134121|Transcript|ENST00000461289.2|lncRNA||||||||||rs1247101959|23|1||HGNC|HGNC:1939||2||||||||||||,G|missense_variant|MODERATE|CHL1|ENSG00000134121|Transcript|ENST00000620033.4|protein_coding|1/25||||99|5|2|E/G|gAg/gGg|rs1247101959||1||HGNC|HGNC:1939||1|A1|deleterious_low_confidence(0.02)|benign(0)|||||||||
4	125638	4_125638_A/T	A	T	.	.	CSQ=T|intron_variant|MODIFIER|ZNF718|ENSG00000250312|Transcript|ENST00000510175.6|protein_coding||1/3||||||||||1||HGNC|HGNC:26889|NM_001039127.6|1|P1|||||||||||,T|intron_variant|MODIFIER|ZNF718|ENSG00000250312|Transcript|ENST00000609714.1|protein_coding||1/3||||||||||1||HGNC|HGNC:26889||1||||||||||||,T|intron_variant&NMD_transcript_variant|MODIFIER|ZNF718|ENSG00000250312|Transcript|ENST00000642529.1|nonsense_mediated_decay||1/4||||||||||1||HGNC|HGNC:26889||||||||||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000164660|promoter|||||||||||||||||||||||||||||
5	145726	5_145726_C/T	C	T	.	.	CSQ=T|intron_variant|MODIFIER|PLEKHG4B|ENSG00000153404|Transcript|ENST00000283426.11|protein_coding||4/17||||||||rs1019159019||1||HGNC|HGNC:29399||1|A2|||||||||||,T|upstream_gene_variant|MODIFIER|Y_RNA|ENSG00000199540|Transcript|ENST00000362670.1|misc_RNA||||||||||rs1019159019|1529|-1||RFAM|||||||||||||||,T|intron_variant|MODIFIER|PLEKHG4B|ENSG00000153404|Transcript|ENST00000502646.1|protein_coding||4/8||||||||rs1019159019||1|cds_start_NF|HGNC|HGNC:29399||1||||||||||||,T|intron_variant|MODIFIER|PLEKHG4B|ENSG00000153404|Transcript|ENST00000637938.1|protein_coding||6/19||||||||rs1019159019||1||HGNC|HGNC:29399||5|P2|||||||||||