SACGF / SACGF/variantgrid

Summary table of ClinGen gene-specific guidelines.

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#115 1 comment 0 reactions 2 assignees Claimed by @TheMadBug View on GitHub
enhancement
Dominant language
Python
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9h 28m
Merged PRs (30d)
42

Description

**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.

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