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)
|