[ensembl-dev] CNV IMPACT
AMANDINE SEPTIER
amandine.septier at univ-grenoble-alpes.fr
Thu Oct 28 08:44:25 BST 2021
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
[ callto:4 146867498 | 4 146867498 ] TTC29_HetDEL . <DEL> . . SVTYPE=DEL;END=146867583 GT:CN 0/1:1 ./.:2 ./.:2
[ callto:12 121908103 | 12 121908103 ] CFAP251_AllGene . <DEL> . . SVTYPE=DEL;END=122003919 GT:CN 1/1:0 1/1:0 1/1:0
[ callto:12 121999716 | 12 121999716 ] CFAP251_HomoDEL . <DEL> . . SVTYPE=DEL;END=122001598 GT:CN 1/1:0 1/1:0 1/1:0
[ callto:12 121999716 | 12 121999716 ] CFAP251_exon20/22 . <DEL> . . SVTYPE=DEL;END=121999944 GT:CN 1/1:0 1/1:0 1/1:0
[ callto:12 122001497 | 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=" [ callto:2021-10-27 11 | 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
[ callto:4 146867498 | 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
[ callto:12 121908103 | 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
[ callto:12 121999716 | 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
[ callto:12 121999716 | 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
[ callto:12 122001497 | 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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