Annotations

The ANNOTATIONS database holds reference data for genomic variant interpretation, deployed in all three environments. Annotation runs through VEP-rs (a Rust VEP), producing all-transcripts annotations for the variant pipelines.

Overview

Annotation reference sets are versioned and live in their own database so the variant pipelines can join calls to interpretation data without bloating CLINICOGENOMICS. The annotated variant tables in VARIANTS (for example VARIANT_CALLS_ANNOTATED_OH_GRCH37) are produced by joining raw calls to these reference sets.

Reference sets

Source	Purpose
gnomAD	Population allele frequencies.
ClinVar	Clinical significance of variants.
CADD	Deleteriousness scoring.
REVEL	Missense pathogenicity scoring.
AlphaMissense	Deep-learning missense pathogenicity prediction.
VEP	Variant Effect Predictor consequence annotations.