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SACGF / variantgrid

VariantGrid public repo
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Summary table of ClinGen gene-specific guidelines. #115

Open sksmi opened 3 years ago

sksmi commented 3 years ago

Background Currently there are 21+ gene-specific modifications of the ACMG guidelines that should be consulted when curating to determine gene-specific thresholds for each criterion. For example, 16 probands (AD inheritance) are required to apply PS4 for POLG, 4 are required for RUNX1 and a Clevland clinic score of >4 is required for PTEN. To speed up curation and inform selection of appropriate thresholds in variant filtering, I've manually developed a quick reference spreadsheet summarising the relevant per-gene thresholds: https://docs.google.com/spreadsheets/d/1XFVe4ILwIBJb8IfJINsUmxYGg4Rrvr6Iep8zGMEqRNc/edit?usp=sharing

Given that it is a considerable effort and responsibility to maintain the table it makes sense to share this with other curators through either VariantGrid or Shariant.

Describe the solution you'd like Is it possible to add the table as a searchable page in VariantGrid (or Shariant if more appropriate?).

Additional context There are multiple benefits in having a high-quality gene table embedded within VariantGrid as this information can be used to auto-populate and calculate gene classifications. It would also be worthwhile contacting ClinGen as it would be better if this resource was available through the ClinGen API.

sksmi commented 3 years ago

Discussed with Alicia. Steven has a version of this already (excel based) for the same reason. Will discuss whether collab is possible.