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clinical-variant-prioritizer

Prioritizes carried genetic variants by ClinVar significance, gnomAD frequency, inheritance, and zygosity.

1.1k|257|Updated Feb 25, 2026
Search Tags:#clinvar#acmg#clinical genomics#gnomad#pathogenicity#variant prioritization#carrier screening
One-click install
npx skills add https://github.com/ClawBio/ClawBio --skill clinical-variant-prioritizer
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: clinical-variant-prioritizer
Source: https://github.com/ClawBio/ClawBio/tree/main/skills/clinical-variant-prioritizer
Command: npx skills add https://github.com/ClawBio/ClawBio --skill clinical-variant-prioritizer

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Raw ClinVar lookups report a label without context, so a heterozygous carrier of a recessive allele can look as alarming as a dominant pathogenic finding. This Skill screens a genotype set against curated OMIM-morbid, ACMG-SF, and Hereditary-Cancer panels and ranks carried variants by actual clinical actionability, following the pathogenicity-screening method of Corpas et al. 2021.

Core Features & Use Cases

  • Panel-Based Screening: Intersects input genotypes with a curated offline panel of catalogued clinical loci carrying ClinVar significance, review status, gnomAD frequency, condition, and inheritance model.
  • Actionability Classification: Categorizes each variant as actionable, affected, carrier, uncertain, benign, or reference based on zygosity and inheritance, with a plain-language rationale for every finding.
  • Ranked Findings Report: Returns findings sorted by clinical priority plus a summary of loci tested, carried, and flagged, with a headline conclusion.
  • Use Case: A researcher with consumer array genotype data (e.g., rsid-to-genotype dict) wants to know which carried variants warrant clinical follow-up versus which are benign carrier states, without per-call ClinVar or gnomAD network queries.

Quick Start

Ask the AI to screen your genotype data against the clinical variant panel and list any actionable or carrier findings ranked by priority.

Frequently Asked Questions about clinical-variant-prioritizer

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I prioritize pathogenic variants from genotype data?▼

Pass a dictionary mapping rsids to genotypes into the run() function, which screens them against a curated clinical panel. Variants are classified by ClinVar significance, gnomAD frequency, inheritance, and zygosity, then ranked so actionable and affected findings appear first.

What gene panels does this variant screening use?▼

The screen uses OMIM-morbid, ACMG Secondary Findings, and Hereditary-Cancer panels stored in a curated clinical_panel.json file. Each entry ships ClinVar significance, review status, gnomAD frequency, condition, and inheritance model, and you can extend it with custom entries.

Does variant prioritization require internet access to ClinVar or gnomAD?▼

No, the panel ships all catalogued annotations locally so the screen is deterministic and offline-reproducible. There are no per-call network round-trips to ClinVar, gnomAD, or VEP.

Why is a heterozygous pathogenic variant not flagged as actionable?▼

For recessive inheritance genes, a heterozygous call means carrier status, which is reproductive-risk relevant but not personally actionable. Only homozygous recessive or dominant/risk-gene pathogenic alleles are classified as affected or actionable.

What are the limitations of array-based variant screening?▼

Array-based input covers only catalogued loci and misses most rare variants, so a clean screen is not a clean genome. Heterozygous calls do not establish phase, and any finding should be confirmed with an accredited clinical assay.

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