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)