The Evidence View

SOP Section 4

Evidence tab organization

The Evidence View is accessible to any logged in curator. It includes both aggregated external evidence and evidence curated manually by individual curators. Please note: you cannot curate from the evidence view .

Using the evidence view alone will not create a variant curation record on your dashboard. To create a record on the dashboard you must start an interpretation.

Once you are in the “Evidence View,” you will see the information and evidence for the selected variant organized into six tabs: Basic Information, Population, Variant Type, Experimental, Case/Segregation, and Gene-centric.

The Variant Type tab is further divided into four subtabs: Missense, Loss of Function, Silent & Intron, and In-frame Indel.

Variant Titles

HGVS variant titles are assigned to variants as follows:

  1. The HGVS is based on the MANE Select transcript if there is one.

  2. If there is no MANE Select transcript, then the HGVS is based on the ClinVar variant title.

  3. If 1 and 2 do not exist, then the HGVS is based on the RefSeq canonical transcript.

  4. If 1-3 do not exist, the HGVS is based on the GRCh38 genomic coordinates.

Evidence types

The Evidence View displays two main types of evidence.

1. External Evidence

The curation interface aggregates dozens of types of evidence from external resources such as gnomAD, PAGE, REVEL, ESP, ClinVar, dbNSFP, etc.

2. Manually curated evidence

  • Evidence a curator enters for a PubMed ID (PMID) or clinical/research sources when in Interpretation mode (see next section) will be viewable by all curators in the Evidence View.

Note: Evaluations (e.g. PS4 “Met”) and Interpretations are specific to the curator who makes them and are not viewable in the Evidence View.

See information on manually adding Case Segregation Data and Functional Data evidence types.

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