[ensembl-dev] CNV IMPACT
Diana Lemos
dlemos at ebi.ac.uk
Thu Oct 28 13:38:49 BST 2021
Hi Amandine,
The IMPACT column is a subjective classification of the severity of the
variant consequence. It is a separate rating given for compatibility
with other variant annotation tools e.g. snpEff. As this rating is
subjective, you can always get the full set of consequences for each
allele and make your own severity judgement.
Information on all of our consequences can be found here:
https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html
<https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html>
Best wishes,
Diana
On 28/10/2021 08:44, AMANDINE SEPTIER wrote:
> Hello VEP team,
>
> Thank you very much for your tool.
> I send you this mail because I'm analyzing Exome data and making CNV
> calls on a patients cohort.
> When I annotate SVs with VEP, it returns "MODIFIER" hits for CNVs
> covering several exons/introns without covering the entire impacted
> gene(s).(details below)
> Some of them are experimentally validated, so it is a pity that VEP
> doesn't send back these CNVs. (ex : CFAP251)
> Is it possible to put more weight on the 'feature_truncation' or
> 'feature_elongation' variants consequences so that they have a greater
> impact?
> This is just a discussion I'm opening up.
> Thanks in advance for your future return.
> Regards.
> --
> ----------------------------------------------------------------------
> Amandine SEPTIER
> Doctorante
> Laboratoire TIMC-IMAG/MAGe, CNRS UMR 5525
> Pavillon Taillefer, Faculté de Médecine
> 38700 La Tronche, France
> ---------------------------------------------------------------
>
> VCF INPUT:
> ##fileformat=VCFv4.3
> ##fileDate=20211027
> ##ALT=<ID=DEL,Description="Deletion">
> ##ALT=<ID=DUP,Description="Duplication">
> ##ALT=<ID=CNV,Description="Copy number variable region">
> ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural
> variant">
> ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the
> variant described in this record">
> ##FORMAT=<ID=GT,Number=1,Type=Integer,Description="Genotype">
> ##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number
> genotype for imprecise events">
> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
> S1 S2 S3
> 4 146867498 <callto:4 146867498> TTC29_HetDEL . <DEL> .
> . SVTYPE=DEL;END=146867583 GT:CN 0/1:1 ./.:2 ./.:2
> 12 121908103 <callto:12 121908103> CFAP251_AllGene . <DEL>
> . . SVTYPE=DEL;END=122003919 GT:CN 1/1:0 1/1:0 1/1:0
> 12 121999716 <callto:12 121999716> CFAP251_HomoDEL . <DEL>
> . . SVTYPE=DEL;END=122001598 GT:CN 1/1:0 1/1:0 1/1:0
> 12 121999716 <callto:12 121999716> CFAP251_exon20/22 .
> <DEL> . . SVTYPE=DEL;END=121999944 GT:CN 1/1:0 1/1:0 1/1:0
> 12 122001497 <callto:12 122001497> CFAP251_exon21/22 .
> <DEL> . . SVTYPE=DEL;END=122001598 GT:CN 1/1:0 1/1:0 1/1:0
>
> COMMAND LINE:
> vep -i VEPtest_211027.vcf --cache --offline --force_overwrite --format
> vcf --vcf -o OutVEP_211027.csv
>
> OUTPUT
> ##fileformat=VCFv4.3
> ##fileDate=20211027
> ##ALT=<ID=DEL,Description="Deletion">
> ##ALT=<ID=DUP,Description="Duplication">
> ##ALT=<ID=CNV,Description="Copy number variable region">
> ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural
> variant">
> ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the
> variant described in this record">
> ##FORMAT=<ID=GT,Number=1,Type=Integer,Description="Genotype">
> ##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number
> genotype for imprecise events">
> ##VEP="v104" time="2021-10-27 11 <callto:2021-10-27 11>:56:04"
> cache="/home/septiera/.vep/homo_sapiens/104_GRCh38"
> ensembl-funcgen=104.59ae779 ensembl-variation=104.6154f8b
> ensembl=104.1af1dce ensembl-io=104.1d3bb6e 1000genomes="phase3"
> COSMIC="92" ClinVar="20210102" ESP="V2-SSA137" HGMD-PUBLIC="20204"
> assembly="GRCh38.p13" dbSNP="154" gencode="GENCODE 38"
> genebuild="2014-07" gnomAD="r2.1.1" 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">
> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
> S1 S2 S3
> 4 146867498 <callto:4 146867498> TTC29_HetDEL . <DEL> .
> .
> SVTYPE=DEL;END=146867583;CSQ=deletion|frameshift_variant&feature_truncation|HIGH|TTC29|ENSG00000137473|Transcript|ENST00000325106|protein_coding|8/13||||1009-1093|800-884|267-295|||||-1||HGNC|HGNC:29936,deletion|frameshift_variant&feature_truncation|HIGH|TTC29|ENSG00000137473|Transcript|ENST00000504425|protein_coding|8/13||||1027-1111|800-884|267-295|||||-1||HGNC|HGNC:29936,deletion|frameshift_variant&NMD_transcript_variant&feature_truncation|HIGH|TTC29|ENSG00000137473|Transcript|ENST00000508306|nonsense_mediated_decay|8/14||||978-1062|800-884|267-295|||||-1||HGNC|HGNC:29936,deletion|frameshift_variant&feature_truncation|HIGH|TTC29|ENSG00000137473|Transcript|ENST00000513335|protein_coding|9/14||||1078-1162|878-962|293-321|||||-1||HGNC|HGNC:29936
> GT:CN 0/1:1 ./.:2 ./.:2
> 12 121908103 <callto:12 121908103> CFAP251_AllGene . <DEL>
> . .
> SVTYPE=DEL;END=122003919;CSQ=deletion|stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation|HIGH|PSMD9|ENSG00000110801|Transcript|ENST00000261817|protein_coding|5-6/6|4-5/5||||||||||1||HGNC|HGNC:9567,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000288912|protein_coding||||||||||||1||HGNC|HGNC:28506,deletion|transcript_ablation|HIGH|PSMD9|ENSG00000110801|Transcript|ENST00000361485|retained_intron||||||||||||1||HGNC|HGNC:9567,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000397454|protein_coding||||||||||||1||HGNC|HGNC:28506,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000428465|retained_intron||||||||||||1||HGNC|HGNC:28506,deletion|non_coding_transcript_exon_variant&feature_truncation|MODIFIER|RNU7-170P|ENSG00000239082|Transcript|ENST00000459303|snRNA|1/1||||2-?|||||||1||HGNC|HGNC:45704,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000535257|retained_intron||||||||||||1||HGNC|HGNC:28506,deletion|3_prime_UTR_variant&intron_variant&NMD_transcript_variant&feature_truncation|MODIFIER|PSMD9|ENSG00000110801|Transcript|ENST00000535293|nonsense_mediated_decay|4-5/5|3-4/4||||||||||1||HGNC|HGNC:9567,deletion|stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&NMD_transcript_variant&feature_truncation|HIGH|PSMD9|ENSG00000110801|Transcript|ENST00000537407|nonsense_mediated_decay|5-7/7|4-6/6||||||||||1||HGNC|HGNC:9567,deletion|downstream_gene_variant|MODIFIER||ENSG00000255856|Transcript|ENST00000538710|lncRNA|||||||||||3515|-1|||,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000540779|retained_intron||||||||||||1||HGNC|HGNC:28506,deletion|3_prime_UTR_variant&intron_variant&NMD_transcript_variant&feature_truncation|MODIFIER|PSMD9|ENSG00000110801|Transcript|ENST00000540962|nonsense_mediated_decay|4-5/5|3-4/4||||||||||1||HGNC|HGNC:9567,deletion|stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation|HIGH|PSMD9|ENSG00000110801|Transcript|ENST00000541212|protein_coding|5-6/6|4-5/5||||||||||1||HGNC|HGNC:9567,deletion|stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation|HIGH|PSMD9|ENSG00000110801|Transcript|ENST00000542602|protein_coding|3-4/4|2-3/3||||||||||1||HGNC|HGNC:9567,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000543211|retained_intron||||||||||||1||HGNC|HGNC:28506,deletion|3_prime_UTR_variant&intron_variant&NMD_transcript_variant&feature_truncation|MODIFIER|PSMD9|ENSG00000110801|Transcript|ENST00000543699|nonsense_mediated_decay|5-6/6|4-5/5||||||||||1||HGNC|HGNC:9567,deletion|non_coding_transcript_exon_variant&intron_variant&feature_truncation|MODIFIER|PSMD9|ENSG00000110801|Transcript|ENST00000544254|retained_intron|2-3/3|1-2/2||||||||||1||HGNC|HGNC:9567,deletion|non_coding_transcript_exon_variant&intron_variant&feature_truncation|MODIFIER|PSMD9|ENSG00000110801|Transcript|ENST00000544724|retained_intron|3-4/4|2-3/3||||||||||1||HGNC|HGNC:9567,deletion|transcript_ablation|HIGH||ENSG00000256950|Transcript|ENST00000544911|retained_intron||||||||||||1|||,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000545752|processed_transcript||||||||||||1||HGNC|HGNC:28506,deletion|non_coding_transcript_exon_variant&intron_variant&feature_truncation|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000545988|processed_transcript|1-2/2|1/1|||?-484|||||||1||HGNC|HGNC:28506,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000546044|retained_intron||||||||||||1||HGNC|HGNC:28506,deletion|3_prime_UTR_variant&intron_variant&NMD_transcript_variant&feature_truncation|MODIFIER||ENSG00000256950|Transcript|ENST00000546333|nonsense_mediated_decay|4/4|3/3||||||||||1|||
> GT:CN 1/1:0 1/1:0 1/1:0
> 12 121999716 <callto:12 121999716> CFAP251_HomoDEL . <DEL>
> . .
> SVTYPE=DEL;END=122001598;CSQ=deletion|coding_sequence_variant&intron_variant&feature_truncation|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000288912|protein_coding|20-21/22|20/21|||3132-3461|3008-3337|1003-1113|||||1||HGNC|HGNC:28506,deletion|non_coding_transcript_exon_variant&intron_variant&feature_truncation|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000428465|retained_intron|1-2/3|1/2|||2832-3161|||||||1||HGNC|HGNC:28506,deletion|upstream_gene_variant|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000545988|processed_transcript|||||||||||106|1||HGNC|HGNC:28506
> GT:CN 1/1:0 1/1:0 1/1:0
> 12 121999716 <callto:12 121999716> CFAP251_Corrpad_exon20/22
> . <DEL> . .
> SVTYPE=DEL;END=121999944;CSQ=deletion|inframe_deletion&feature_truncation|MODERATE|CFAP251|ENSG00000158023|Transcript|ENST00000288912|protein_coding|20/22||||3132-3359|3008-3235|1003-1079|||||1||HGNC|HGNC:28506,deletion|non_coding_transcript_exon_variant&feature_truncation|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000428465|retained_intron|1/3||||2832-3059|||||||1||HGNC|HGNC:28506,deletion|upstream_gene_variant|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000545988|processed_transcript|||||||||||1760|1||HGNC|HGNC:28506
> GT:CN 1/1:0 1/1:0 1/1:0
> 12 122001497 <callto:12 122001497> CFAP251_Corrpad_exon21/22
> . <DEL> . .
> SVTYPE=DEL;END=122001598;CSQ=deletion|frameshift_variant&feature_truncation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000288912|protein_coding|21/22||||3361-3461|3237-3337|1079-1113|||||1||HGNC|HGNC:28506,deletion|non_coding_transcript_exon_variant&feature_truncation|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000428465|retained_intron|2/3||||3061-3161|||||||1||HGNC|HGNC:28506,deletion|upstream_gene_variant|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000545988|processed_transcript|||||||||||106|1||HGNC|HGNC:28506
> GT:CN 1/1:0 1/1:0 1/1:0
>
>
> System
>
> * VEP version: 104.3
> * VEP Cache version: homo_sapiens_vep_104_GRCh38
> * Perl version: perl-5.16.3-299.el7_9.x86_64
> * OS: centos 7
> * tabix installed ? yes
>
>
>
> _______________________________________________
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