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