The new Ensembl Variant Effect Predictor (Ensembl VEP) web interface now has more extensive options for variants on the human GRCh38 assembly, including allele frequencies, phenotype associations and variant impact scores.
The new website enables basic analysis of variants in VCF format from any of the assemblies held in Ensembl, including hundreds of human haplotype assemblies from the Human Pangenome Reference Consortium. Our latest update brings in loads more options for variants on the current human reference including:
- Missense variant impact predictions from AlphaMissense, REVEL, ClinPred and EVE
- Predictions of impact on splicing from SpliceAI
- Genome-wide predictions of tolerance to change from CADD
- GERP conservation scores
- Allele frequencies from gnomAD and NIH All of Us
- Predictions of NMD escape, impact on UTRs and non canonical open reading frames
- Phenotype associations from sources including ClinVar, GWAS Catalog and GenCC
- Gene function annotations from the Gene Ontology
- HGVS protein and transcript descriptions
- LOEUF and pLI gene constraint measures and dosage sensitivity estimates from gnomAD
- Functional assay results from MaveDB and IntAct
Click on the ‘ENSVEP’ icon on any Ensembl page to try it out!
Example results for variant: 1 230710048 . A C
We are making continuous updates to the new platform and more Ensembl VEP analysis options (including regulatory effect, names from other resources and more detailed protein annotations) will be added for human and other species in coming weeks. In the meantime if you are missing your favourite features, the classic version of Ensembl VEP is still available via our archives. Thanks for your patience as we migrate to our new platform!
Authored by: Sarah Hunt
Reviewed by: Louisse Paola Mirabueno