# Clinical Variant Prioritizer

Screen a genotype set (array or WGS-derived) against OMIM-morbid, ACMG-SF and...

- Repository: https://github.com/ClawBio/ClawBio (1172 stars)
- Category: Engineering
- License: MIT
- Last updated: 2026-11-01
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add ClawBio/ClawBio --skill clinical-variant-prioritizer -g -a claude-code -y`
Codex: `npx skills add ClawBio/ClawBio --skill clinical-variant-prioritizer -g -a codex -y`
Cursor: `npx skills add ClawBio/ClawBio --skill clinical-variant-prioritizer -g -a cursor -y`
Gemini CLI: `npx skills add ClawBio/ClawBio --skill clinical-variant-prioritizer -g -a gemini-cli -y`
Claude Code plugin marketplace: `/plugin marketplace add ClawBio/ClawBio`

## Description

Screen a genotype set (array or WGS-derived) against OMIM-morbid, ACMG-SF and Hereditary-Cancer gene panels and prioritise carried variants by ClinVar significance, gnomAD frequency, inheritance model and zygosity, following the pathogenicity-screening method of Corpas et al. 2021 (Whole Genome Interpretation for a Family of Five).

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# clinical-variant-prioritizer

Turn a genotype set into a prioritised list of clinically relevant variants, the
way a clinical genome analyst would: screen catalogued disease-gene panels,
then rank what is carried by **how much it matters**, not by how loud the raw
ClinVar label is.

This skill implements the pathogenicity-screening stage of *Whole Genome
Interpretation for a Family of Five* (Corpas et al., Front Genet 2021): variants
are filtered through **OMIM-morbid**, **ACMG-SF** and **Hereditary-Cancer**
panels, intersected with **ClinVar** significance and **gnomAD** population
frequency, and classified by **inheritance model** and **zygosity**.

## Why it is not a raw ClinVar lookup

A raw lookup reports a label. This skill reports *actionability*. The same
"pathogenic" allele means very different things depending on context:

| Context | Category |
|---|---|
| Dominant / risk gene, allele carried | `actionable` |
| Recessive gene, homozygous | `affected` |
| Recessive gene, heterozygous | `carrier` (reproductive-risk only) |
| Uncertain / conflicting ClinVar | `uncertain` (flagged, not acted on) |
| Benign allele carried | `benign` |
| Variant not carried | `reference` |

A heterozygous carrier of a common, recessive, benign-spectrum allele is *not*
an actionable finding, even when ClinVar shows "pathogenic" submissions. Saying
so plainly is the point.

## Interface

```python
from api import run

result = run(
    {"rs28941785": "CT", "rs1800562": "GG"},   # rsid -> genotype
    options={"panel_path": "..."},              # optional custom panel
)
```

`run()` returns:

The rest: https://github.com/ClawBio/ClawBio/blob/HEAD/skills/clinical-variant-prioritizer/SKILL.md