gnomad-mcp

TGG Claude Code Plugins

Plugin marketplace for the Translational Genomics Group, providing genomics analysis capabilities for Claude Code.

Installation

Add the marketplace to Claude Code:

/plugin marketplace add /path/to/tgg-llm-plugins

Or via GitHub (once pushed):

/plugin marketplace add your-org/tgg-llm-plugins

Available Plugins

variant-interpreter

Interpret variant pathogenicity from gnomAD CSV exports using ACMG/AMP guidelines.

Install:

/plugin install variant-interpreter@tgg-plugins

Usage:

/variant-interpret

Then provide the path to your gnomAD CSV file when prompted.

Data Preparation:

1. Go to gnomAD browser
2. Search for your gene of interest
3. Click "Export variants to CSV"
4. Download to your working directory

Features:

• Parse gnomAD CSV exports directly (no API required)
• Population frequency analysis with ACMG/AMP thresholds (BA1, BS1)
• Disease-specific maximum credible allele frequency calculation (Whiffin et al.)
• In silico prediction synthesis with gnomAD-calibrated thresholds:
  • REVEL (0.644/0.773)
  • CADD (25.3/28.1)
  • SpliceAI (0.2/0.5)
  • Pangolin (0.2/0.5)
  • phyloP (7.367/9.741)
• ClinVar classification review
• Quality flag assessment
• Population-specific frequency analysis

Development

Directory Structure

tgg-llm-plugins/
├── .claude-plugin/
│   └── marketplace.json          # Marketplace catalog
└── plugins/
    └── variant-interpreter/
        ├── .claude-plugin/
        │   └── plugin.json       # Plugin manifest
        └── skills/
            └── variant-interpret/
                └── SKILL.md      # Skill definition

Adding New Plugins

1. Create a new directory under plugins/
2. Add .claude-plugin/plugin.json with plugin metadata
3. Add skills, hooks, or other components as needed
4. Register the plugin in .claude-plugin/marketplace.json

License

Internal use - Translational Genomics Group