gnomAD MCP server

This MCP server provides access to the gnomAD (Genome Aggregation Database) GraphQL API, allowing AI assistants to query genetic variant data, gene constraints, and population genetics information directly from gnomAD.

Installation

Prerequisites

• Node.js 18 or higher
• npm or yarn

Setting Up the Server

git clone https://github.com/yourusername/gnomad-mcp-server.git
cd gnomad-mcp-server
npm install
npm run build

Configuration

Configuring for Claude Desktop

Add the server to your Claude Desktop configuration file:

macOS:

~/Library/Application Support/Claude/claude_desktop_config.json

Windows:

%APPDATA%\Claude\claude_desktop_config.json

Add the following JSON configuration:

{
  "mcpServers": {
    "gnomad": {
      "command": "node",
      "args": ["/path/to/gnomad-mcp-server/dist/index.js"]
    }
  }
}

Using with MCP CLI

Alternatively, you can run the server using the MCP CLI:

npx @modelcontextprotocol/cli gnomad-mcp-server

Available Tools

Search Tool

The search tool allows you to search for genes, variants, or regions in gnomAD.

Parameters:

• query (required): Search query (gene symbol, gene ID, variant ID, rsID)
• reference_genome: Reference genome (GRCh37 or GRCh38, default: GRCh38)
• dataset: Dataset ID (gnomad_r4, gnomad_r3, gnomad_r2_1, etc., default: gnomad_r4)

Example:

{
  "query": "TP53",
  "reference_genome": "GRCh38"
}

Gene Information Tool

The get_gene tool retrieves detailed information about a gene including constraint scores.

Parameters:

• gene_id: Ensembl gene ID (e.g., ENSG00000141510)
• gene_symbol: Gene symbol (e.g., TP53)
• reference_genome: Reference genome (default: GRCh38)

Example:

{
  "gene_symbol": "BRCA1",
  "reference_genome": "GRCh38"
}

Variant Information Tool

The get_variant tool provides detailed information about a specific variant.

Parameters:

• variant_id (required): Variant ID in format: chr-pos-ref-alt
• reference_genome: Reference genome (default: GRCh38)
• dataset: Dataset ID (default: gnomad_r4)

Example:

{
  "variant_id": "13-32339421-G-A",
  "reference_genome": "GRCh38"
}

Features

The gnomAD MCP Server provides access to:

• Gene Information: Search and retrieve detailed gene data including constraint scores
• Variant Analysis: Query specific variants and their population frequencies
• Population Genetics: Access allele frequencies across different populations
• Constraint Scores: Get pLI, LOEUF, and other constraint metrics
• Region Queries: Find variants within specific genomic regions
• Transcript Data: Access transcript-specific information and constraints
• Coverage Data: Retrieve sequencing coverage statistics
• Structural Variants: Query structural variant data
• Mitochondrial Variants: Access mitochondrial genome variants

How to install this MCP server

For Claude Code

To add this MCP server to Claude Code, run this command in your terminal:

claude mcp add-json "gnomad" '{"command":"node","args":["/path/to/gnomad-mcp-server/dist/index.js"]}'

See the official Claude Code MCP documentation for more details.

For Cursor

There are two ways to add an MCP server to Cursor. The most common way is to add the server globally in the ~/.cursor/mcp.json file so that it is available in all of your projects.

If you only need the server in a single project, you can add it to the project instead by creating or adding it to the .cursor/mcp.json file.

Adding an MCP server to Cursor globally

To add a global MCP server go to Cursor Settings > Tools & Integrations and click "New MCP Server".

When you click that button the ~/.cursor/mcp.json file will be opened and you can add your server like this:

{
    "mcpServers": {
        "gnomad": {
            "command": "node",
            "args": [
                "/path/to/gnomad-mcp-server/dist/index.js"
            ]
        }
    }
}

Adding an MCP server to a project

To add an MCP server to a project you can create a new .cursor/mcp.json file or add it to the existing one. This will look exactly the same as the global MCP server example above.

How to use the MCP server

Once the server is installed, you might need to head back to Settings > MCP and click the refresh button.

The Cursor agent will then be able to see the available tools the added MCP server has available and will call them when it needs to.

You can also explicitly ask the agent to use the tool by mentioning the tool name and describing what the function does.

For Claude Desktop

To add this MCP server to Claude Desktop:

1. Find your configuration file:

• macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
• Windows: %APPDATA%\Claude\claude_desktop_config.json
• Linux: ~/.config/Claude/claude_desktop_config.json

2. Add this to your configuration file:

{
    "mcpServers": {
        "gnomad": {
            "command": "node",
            "args": [
                "/path/to/gnomad-mcp-server/dist/index.js"
            ]
        }
    }
}

3. Restart Claude Desktop for the changes to take effect