Annotation refers to all of the information about a variant, it is made from different components, including:
Variant-level annotation: Information specific to a base change. Examples include computational predictions and effects, and existing database entries (such as population frequency for the variant)
Gene-level annotation: Information about the gene (from RefSeq/Ensembl + other sources), matched from the variant’s assigned transcript_id.
ClinVar: Clinical variant classifications from ClinVar
To see a description of each field, use menu: [annotation] -> [descriptions]
Variant Level Annotation¶
The first time we see a variant, it is annotated by Ensembl Variant Effect Predictor (VEP) and then cached in the database.
To see the VEP fields used, check the “Show Ensembl Variant Effect Predictor source fields” checkbox on the annotation descriptions ([annotation] -> [descriptions]) page.
Each annotation component above is versioned and can be upgraded separately by the site administrator. To see the versions via menu: [annotation] -> [versions]
VariantGrid can store multiple annotation versions, which allows us to load historical analyses which return the same results as when they were first analysed, as well as updating from new sources regularly.