When you find a variant you are interested in, you will want to thoroughly investigate all current knowledge about it. For each Ensembl release we update our variation databases with the latest public information from a wide range of resources and make summary information available in VEP. We now make it easier to link to fuller details in these resources by providing lists of names used for each variant in each.

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The web VEP tool gives you a lot of useful information about your variants, but you may want more details, for example about the genes your variants overlap: maybe you want to fetch their sequences, homologues or protein domains. With a single click, you can go straight to BioMart, using your list of genes or known variants as your filter.

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Allele frequency data is important for variant prioritisation – it helps to identify variants that are less likely to be causing a phenotype or disease. With the Ensembl VEP, you can get allele frequencies for variants that are identical with the variants you analysed and you can use allele frequencies to filter the results of your analysis.

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Variants can be represented in myriad different ways; indeed, Ensembl VEP currently supports input in many different formats, including VCF, HGVS and SPDI. However, even within these specifications, variants can be described ambiguously. Insertions and deletions within repeated regions can be described at multiple different locations. For example, VCF describes variants using their most 5’ representation, while HGVS format describes a variant at its most 3’ location. 

Starting in Ensembl 100, VEP optionally normalises variants within repeated regions by shifting them as far as possible in the 3’ direction before consequence calculation. This standardises VEP output for equivalent variant alleles which are described using different conventions. 

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