# Gnomad (npm · @pipeworx/mcp-gnomad)

gnomAD MCP — Broad Institute Genome Aggregation Database (GraphQL).

- Trust score: 80/100 (high trust)
- Change this week: +3
- Registry status: active
- Liveness: live
- Owner verified: no
- Last scored: 2026-11-05

## Components

- remote · `gateway.pipeworx.io`: 77/100, [markdown](https://verifymcp.io/servers/pipeworx-io-gnomad/gnomad-mcp.md), [page](https://verifymcp.io/servers/pipeworx-io-gnomad/gnomad-mcp)
- npm · `@pipeworx/mcp-gnomad`: 80/100 (this document), [markdown](https://verifymcp.io/servers/pipeworx-io-gnomad/pipeworx-mcp-gnomad.md), [page](https://verifymcp.io/servers/pipeworx-io-gnomad/pipeworx-mcp-gnomad)

## Channel facts

- Registry: `npm`
- Package: `@pipeworx/mcp-gnomad`
- Version: `0.2.1`
- Transport: `stdio`

## Trust breakdown

How this component scores in each security and reliability category. Every signal is checked automatically from public evidence about the published package, including repeated runs of it in an isolated sandbox, and we only credit what we can confirm. Scores are 0–100 per category. Scoring method: https://verifymcp.io/docs/scoring (what has changed: https://verifymcp.io/docs/scoring/changelog)

Scored 2026-11-05.

- **Supply Chain Security**: 100/100
  - No malware found by supply-chain analysis.
  - No known CVEs affecting this package version or its production dependencies.
  - No install/post-install scripts declared.
  - No production dependencies, so there is no dependency health to assess.
- **Provenance & Transparency**: 97/100
  - Source repository is publicly reachable at the declared URL.
  - Cryptographically verified build provenance (signed, bound to pipeworx-io/mcp-gnomad).
  - Clear OSI-approved license (MIT).
  - Actively maintained (last published 3 days ago).
  - Disclosure check failed: no security disclosure policy was found in the source repository.
- **Schema Quality & AI Usability**: 59/100
  - AI-judged instruction clarity (good).
  - Context-footprint check failed: tool/resource definitions use about 929 tokens (~185/item across 5 items; 5 tools + 0 resources), over budget; trim descriptions and params.
  - Usage-examples check failed: none of the tools include examples.
- **Stability & Change Management**: 23/100
  - Stability observed for 7 of 30 days with no destabilising changes; credit accrues until the full window elapses.
- **Tool Coverage**: 87/100
  - 100% of tools have a non-trivial description (not blank, and not just the tool's name).
  - 61% of tool parameters carry a description.
- **Tool Safety**: 100/100
  - No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.
  - We read all 5 captured tool definition(s), and no name or description among them implies an irreversible operation.
  - An AI judge read all 6 captured unit(s) of tool text and found none that tries to manipulate the model reading it.
- **Capabilities**: 100/100
  - Implements a supported MCP spec version (2025-11-25); the latest is 2026-07-28.

## Install

### How do I install the Gnomad MCP server?

Gnomad runs locally as an npm package, launched with npx -y @pipeworx/mcp-gnomad. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.

### Claude

```bash
claude mcp add pipeworx-io-gnomad -- npx -y @pipeworx/mcp-gnomad
```

### Cursor

```json
{
  "mcpServers": {
    "pipeworx-io-gnomad": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-gnomad"
      ]
    }
  }
}
```

### VS Code

```json
{
  "servers": {
    "pipeworx-io-gnomad": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-gnomad"
      ]
    }
  }
}
```

### Codex

```bash
codex mcp add pipeworx-io-gnomad -- npx -y @pipeworx/mcp-gnomad
```

### opencode

```json
{
  "$schema": "https://opencode.ai/config.json",
  "mcp": {
    "pipeworx-io-gnomad": {
      "type": "local",
      "command": [
        "npx",
        "-y",
        "@pipeworx/mcp-gnomad"
      ],
      "enabled": true
    }
  }
}
```

### OpenClaw

```bash
openclaw mcp add pipeworx-io-gnomad --command npx --arg -y --arg @pipeworx/mcp-gnomad
```

### Hermes

```yaml
mcp_servers:
  pipeworx-io-gnomad:
    command: "npx"
    args: ["-y", "@pipeworx/mcp-gnomad"]
```

### Netclaw

```json
{
  "McpServers": {
    "pipeworx-io-gnomad": {
      "Transport": "stdio",
      "Command": "npx",
      "Arguments": [
        "-y",
        "@pipeworx/mcp-gnomad"
      ]
    }
  }
}
```

### Vellum

```bash
assistant mcp add pipeworx-io-gnomad -t stdio -c npx -a -y @pipeworx/mcp-gnomad
```

### Other

```json
{
  "mcpServers": {
    "pipeworx-io-gnomad": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-gnomad"
      ]
    }
  }
}
```

## Changelog

Every change recorded for this component, newest first. Days that predate change tracking, or that we cannot explain, say so: "we were watching and nothing happened" and "we were not watching" are different claims.

### 2026-11-04 (score 80, +1)

No change was recorded against any check on this day. Stability & Change Management went from 17 to 20. That category is still filling its 30-day observation window: 5 days of observed history at the previous scan, 6 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-11-03 (score 79, 0)

- [functional regression] Security disclosure: unverified → fail

### 2026-11-02 (score 79, +2)

- [functional regression] Security disclosure: fail → unverified
- [functional improvement] Stability: unverified → 0.13
- [functional] Package version: 0.2.0 → 0.2.1

### 2026-10-29 (score 77)

First indexed and scored.

## MCP tools (5)

### `variant` (~111 tokens)

Variant by chr-pos-ref-alt (e.g. "1-55051215-G-A") or rsid (e.g. "rs1801133"). Coordinates must match the dataset's genome build: the default gnomad_r4 is GRCh38, so a GRCh37/hg19 position will not be found — pass dataset "gnomad_r2_1" for GRCh37.

Input parameters:

- `dataset` (string): Default gnomad_r4.
- `variant_id` (string, required)

### `gene` (~165 tokens)

Gene info + its variants. Accepts gene symbol (e.g. "BRCA1") or Ensembl gene id. Variants are paged (default 500, max 2,000 per call); variants_page gives the exact total and next_offset.

Input parameters:

- `dataset` (string)
- `gene_symbol_or_id` (string, required)
- `limit` (number): Variants to return, 1-2000. Default 500. gnomAD returns every variant with no limit of its own (BRCA1 has ~7,300), so the list is paged here; variants_page says how many exist and the next offset.
- `offset` (number): Skip this many variants first, for the next page (variants_page.next_offset). Default 0.

### `region` (~342 tokens)

Variants in a genomic region (≤25kb recommended). You MUST say which genome build your start/stop are in via assembly — there is no default, because a position is valid in both builds and a wrong guess returns real variants from the wrong locus rather than an error. Variants are paged (default 500, max 2,000 per call); variants_page gives the exact total and next_offset.

Input parameters:

- `assembly` (string, required): REQUIRED. The genome build your start/stop are in: "GRCh38" (= hg38) or "GRCh37" (= hg19). There is no default, because every position is valid in both builds — an unstated build cannot be detected,…
- `chrom` (string, required): e.g. "1", "X", "MT"
- `dataset` (string): Default gnomad_r4 (GRCh38). gnomad_r2_1* and exac are GRCh37.
- `limit` (number): Variants to return, 1-2000. Default 500. gnomAD returns every variant with no limit of its own (BRCA1 has ~7,300), so the list is paged here; variants_page says how many exist and the next offset.
- `offset` (number): Skip this many variants first, for the next page (variants_page.next_offset). Default 0.
- `start` (number, required)
- `stop` (number, required)

### `transcript` (~188 tokens)

Fetch gnomAD variant data for an Ensembl transcript (ENST…), returning transcript coordinates, gene symbol, chromosome position, and per-variant allele counts (ac/an) from exome and genome datasets. Variants are paged (default 500, max 2,000 per call); variants_page gives the exact total and next_offset.

Input parameters:

- `dataset` (string)
- `limit` (number): Variants to return, 1-2000. Default 500. gnomAD returns every variant with no limit of its own (BRCA1 has ~7,300), so the list is paged here; variants_page says how many exist and the next offset.
- `offset` (number): Skip this many variants first, for the next page (variants_page.next_offset). Default 0.
- `transcript_id` (string, required): Ensembl transcript id (ENST…)

### `search` (~68 tokens)

Autocomplete-style search across gnomAD genes and variants by free-text query; returns matching Ensembl gene IDs with symbols, and matching variant IDs (an rsid resolves here). Use to resolve a partial gene name, symbol or rsid before calling gene or variant.

Input parameters:

- `query` (string, required)

## Diagnostics

Captured diagnostic sections: Provenance, Dependencies. The full working is on the page: https://verifymcp.io/servers/pipeworx-io-gnomad/pipeworx-mcp-gnomad#diagnostics

## Score history

- 2026-11-05: 80
- 2026-11-04: 80
- 2026-11-03: 79
- 2026-11-02: 79
- 2026-11-01: 77
- 2026-10-31: 77
- 2026-10-30: 77
- 2026-10-29: 77

## Common questions

### What is the Gnomad MCP server?

Gnomad is an MCP server listed in the public MCP registry as io.github.pipeworx-io/gnomad. gnomAD MCP, Broad Institute Genome Aggregation Database (GraphQL). This page covers its npm package (@pipeworx/mcp-gnomad).

### Is the Gnomad MCP server safe to use?

Gnomad scores 80 out of 100 on VerifyMCP. We found no known CVEs affecting it as of 5 November 2026. It declares no install or post-install scripts. Its build provenance is signed and verified. That is a record of what we were able to check automatically, not an endorsement. The category breakdown on this page shows every signal behind the number, including the ones we could not confirm.

### What tools does the Gnomad MCP server expose?

Gnomad exposes 5 tools: variant, gene, region, transcript, search. Their descriptions and schemas cost roughly 874 tokens of context every time the server is loaded.

### Is the Gnomad MCP server still maintained?

Gnomad is still listed as active in the MCP registry. We last reached this channel on 5 November 2026. Those dates come from our own scans of the registry and the channel itself, not from anything the publisher announced.

### What licence is the Gnomad MCP server under?

Gnomad declares the MIT licence, which is OSI-approved. That covers the source only, and says nothing about the cost of any service it calls.

### What did VerifyMCP test on the Gnomad MCP server?

VerifyMCP ran 16 checks on Gnomad, covering Malware scan, Known CVEs, Install scripts, Dependency health and 12 more. Endpoint Security and Transport & Reachability do not apply to an npm package, so they were not tested. The score does not measure everything, and the scoring documentation lists what it leaves out.

## Links

- npm package: https://www.npmjs.com/package/@pipeworx/mcp-gnomad
- Socket report: https://socket.dev/npm/package/@pipeworx/mcp-gnomad
- Repository: https://github.com/pipeworx-io/mcp-gnomad
- Website: https://pipeworx.io/packs/gnomad
- Changelog RSS feed: https://verifymcp.io/servers/pipeworx-io-gnomad/pipeworx-mcp-gnomad.xml
- Changelog JSON feed: https://verifymcp.io/servers/pipeworx-io-gnomad/pipeworx-mcp-gnomad/changelog.json
- Trust report (JSON): https://verifymcp.io/servers/pipeworx-io-gnomad/pipeworx-mcp-gnomad.json
- HTML version of this page: https://verifymcp.io/servers/pipeworx-io-gnomad/pipeworx-mcp-gnomad