Table 2 Major tables in the Reference Variant Store that hold all imported variants and annotations
Table | Description |
|---|---|
Summary | main table that stores each variant by chromosomal location, reference and alternate allele, dbSNP, and GRCh36/38 locations; most other tables are dependent tables |
Impact | effect(s) on gene, transcript, intron/exon, missense/ non-sense, CDS and amino acid change, where applicable; by transcript |
Frequencies | allele frequencies in large-scale sequencing studies (1000 Genomes, ESP6500, ExAC, Scripps Wellderly, etc.) |
Predictions | computational predictions of functional impact, such as PolyPhen-2, MutationAssessor, SIFT, CADD, PROVEAN, GWAVA, and ensemble scores |
Phenotypes | disease-associations from ClinVar, HGMD, OMIM, etc. |
Regions | observed and predicted regions that contain the given variant: functional and regulatory elements (ENCODE), protein domains (InterPro), microRNA target sites (miRanda) |
Source | maps each variant to the study/studies in which it was observed; also stores pass- or non-pass flags according to filtering criteria if provided by the study |
Comments | optional: human expert comments on specific variants, pertaining to disease, impact, etc. |
Staging_summary | registry that holds potentially new variants while they are not yet automatically annotated and copied to the production summary table |
Staging_impact | holds results from computational models regarding effects of the mutation (protein level) |