gnomad-genetics-mcp-server

A community MCP server providing tools to query gnomAD population genetics data and ClinVar clinical significance. It supports retrieving ancestry allele frequencies, gene loss-of-function constraint metrics, variant lists, and sequencing coverage. It also includes SQL querying capabilities for staged data frames.

Package and access

Local package with source-attributed installation metadata. Koskamo does not execute packages during review.

Community listingLocal stdioSource reviewed; not executedPublished by cyanheads

Vendor documentation

What you can do with it

Retrieve per-ancestry allele frequencies for specific variants
Query gene loss-of-function constraint metrics like pLI and LOEUF
List variants in a gene or region with allele frequencies
Run read-only SQL queries against staged gnomAD data frames

Source and maintenance

Community listingRegistry 0.5.0

mcp-registry: io.github.cyanheads/gnomad-genetics-mcp-server@0.5.0 Source repository

Maintenance checked: Oct 31, 2026, 10:59 PM UTC

Packages and installation

Source-provided package data. Koskamo has not executed or live-probed this package.

@cyanheads/gnomad-genetics-mcp-server 0.5.0

npmnpx

@cyanheads/gnomad-genetics-mcp-server package definition

{
  "version": "0.5.0",
  "transport": "stdio",
  "identifier": "@cyanheads/gnomad-genetics-mcp-server",
  "runtimeHint": "npx",
  "registryType": "npm",
  "registryBaseUrl": "https://registry.npmjs.org",
  "environmentVariables": [
    {
      "name": "MCP_LOG_LEVEL",
      "format": "string",
      "default": "info",
      "description": "Sets the minimum log level for output (e.g., 'debug', 'info', 'warn')."
    }
  ]
}

Tools

Reported by the attributed source; not independently observed by Koskamo.

No tool definitions available.

Connect from your client

Each snippet configures the same source-provided package; replace placeholders before use.

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Cursor

Merge this local stdio configuration, replace every placeholder environment value, and restart Cursor. Koskamo has not executed this package.

Cursor configuration

{
  "mcpServers": {
    "gnomad-genetics-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/gnomad-genetics-mcp-server@0.5.0"
      ],
      "env": {
        "MCP_LOG_LEVEL": "<YOUR_MCP_LOG_LEVEL>"
      }
    }
  }
}

Cline

Merge this local stdio configuration, replace every placeholder environment value, and restart Cline. Koskamo has not executed this package.

Cline configuration

{
  "mcpServers": {
    "gnomad-genetics-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/gnomad-genetics-mcp-server@0.5.0"
      ],
      "env": {
        "MCP_LOG_LEVEL": "<YOUR_MCP_LOG_LEVEL>"
      }
    }
  }
}

VS Code

Merge this local stdio configuration, replace every placeholder environment value, and restart VS Code. Koskamo has not executed this package.

VS Code configuration

{
  "servers": {
    "gnomad-genetics-mcp-server": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/gnomad-genetics-mcp-server@0.5.0"
      ],
      "env": {
        "MCP_LOG_LEVEL": "<YOUR_MCP_LOG_LEVEL>"
      }
    }
  }
}

Claude Desktop

Merge this local stdio configuration, replace every placeholder environment value, and restart Claude Desktop. Koskamo has not executed this package.

Claude Desktop configuration

{
  "mcpServers": {
    "gnomad-genetics-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/gnomad-genetics-mcp-server@0.5.0"
      ],
      "env": {
        "MCP_LOG_LEVEL": "<YOUR_MCP_LOG_LEVEL>"
      }
    }
  }
}

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