[ensembl-dev] VEP SV annotation

[Anja Thormann]

Hi Sigurjon,

we developed our IMPACT ratings in collaboration with other variation annotation tools for compatibility reasons and also in order to make it easier to categorize and prioritize variants. The assignments are putative and must be used with care. But we absolutely agree with your feedback and will review and update the assignments accordingly.

Best wishes,
Anja

> On 25 Aug 2021, at 16:30, Sigurjón Axel Guðjónsson <Sigurjon.Gudjonsson at decode.is> wrote:
> 
>  
> Hi,
>  
> I am using VEP to annotate nssv15852771, and I notice that VEP annotates the transcript IMPACT as MODIFIER, but gnomad reports this sv variant as loss of function, https://gnomad.broadinstitute.org/variant/DEL_1_3860?dataset=gnomad_sv_r2_1 <https://gnomad.broadinstitute.org/variant/DEL_1_3860?dataset=gnomad_sv_r2_1>,
> since it knocks out exon 1 which is also coding.
>  
> Here is the vcf output from VEP:
>  
> ##fileformat=VCFv4.1
> ##VEP="v104" time="2021-08-25 14:58:12" cache="/net/isilonP/public/ro/ensweb-data/latest/tools/www/e104/vep/cache/homo_sapiens_refseq/104_GRCh38" db="homo_sapiens_core_104_38 at hh-mysql-ens-species-web-1" 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" refseq="2020-12-10 18:46:50 - GCF_000001405.39_GRCh38.p13_genomic.gff" 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_SELECT|MANE_PLUS_CLINICAL|TSL|APPRIS|REFSEQ_MATCH|REFSEQ_OFFSET|GIVEN_REF|USED_REF|BAM_EDIT|AF|CLIN_SIG|SOMATIC|PHENO|PUBMED">
> #CHROM             POS        ID           REF        ALT        QUAL    FILTER   INFO
> chr1       55029217             nssv15852771    G            <DEL>   .               .              SVTYPE=DEL;END=55043368;SVLEN=-14152;CSQ=deletion|coding_sequence_variant&5_prime_UTR_variant&intron_variant&feature_truncation|MODIFIER|PCSK9|255738|Transcript|NM_174936.4|protein_coding|1/12|1/11||||||||||1||EntrezGene||ENST00000302118.5|||||||||||||,deletion|non_coding_transcript_exon_variant&intron_variant&feature_truncation|MODIFIER|PCSK9|255738|Transcript|NR_110451.2|misc_RNA|1/10|1/9||||||||||1||EntrezGene|||||||||||||||
>  
>  
> Is there any valid reason why VEP does not annotate this as HIGH IMPACT,or is this a bug in VEP ?
>  
> Best regards,
>  
> Sigurjon A. Gudjonsson
> Bioinformatics Group
> Decode Genetics
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