# Myvariant (npm · @pipeworx/mcp-myvariant)

MyVariant.info MCP. Aggregated human genetic-variant annotation: dbSNP, ClinVar clinical…

- Trust score: 81/100 (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-myvariant/myvariant-mcp.md), [page](https://verifymcp.io/servers/pipeworx-io-myvariant/myvariant-mcp)
- npm · `@pipeworx/mcp-myvariant`: 81/100 (this document), [markdown](https://verifymcp.io/servers/pipeworx-io-myvariant/pipeworx-mcp-myvariant.md), [page](https://verifymcp.io/servers/pipeworx-io-myvariant/pipeworx-mcp-myvariant)

## Channel facts

- Registry: `npm`
- Package: `@pipeworx/mcp-myvariant`
- 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-myvariant).
  - Clear OSI-approved license (MIT).
  - Actively maintained (last published 2 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 669 tokens (~223/item across 3 items; 3 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**: 100/100
  - 100% of tools have a non-trivial description (not blank, and not just the tool's name).
  - 100% 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 3 captured tool definition(s), and no name or description among them implies an irreversible operation.
  - An AI judge read all 4 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 Myvariant MCP server?

Myvariant runs locally as an npm package, launched with npx -y @pipeworx/mcp-myvariant. 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-myvariant -- npx -y @pipeworx/mcp-myvariant
```

### Cursor

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

### VS Code

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

### Codex

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

### opencode

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

### OpenClaw

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

### Hermes

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

### Netclaw

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

### Vellum

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

### Other

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

## 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 81, +16)

- [security improvement] Malware scan: unverified → pass

### 2026-11-03 (score 65, −13)

- [security regression] Malware scan: pass → unverified
- [functional improvement] Stability: unverified → 0.17
- [functional] Package version: 0.2.0 → 0.2.1

### 2026-10-30 (score 78, 0)

- [functional regression] Security disclosure: unverified → fail

### 2026-10-29 (score 78)

First indexed and scored.

## MCP tools (3)

### `query` (~313 tokens)

Search aggregated human genetic-variant annotations on MyVariant.info. Accepts an rsID ("rs58991260") or a fielded query ("dbnsfp.genename:CDK2", "clinvar.rcv.clinical_significance:pathogenic"). A bare HGVS id does NOT match here — look one up with the variant tool instead. Each hit merges dbSNP, ClinVar clinical significance, CADD/dbNSFP deleteriousness scores, and gnomAD population allele frequencies. Returns { total, hits, assembly }; hit._id is the HGVS id you can pass to the variant tool, and its coordinates are in the assembly you asked for — hg19 unless you say otherwise.

Input parameters:

- `assembly` (string): Genome build for the coordinates you pass AND the ids you get back: "hg19" (GRCh37, the default) or "hg38" (GRCh38). gnomAD and Ensembl coordinates are GRCh38.
- `fields` (string): Comma-separated return fields (default: all). e.g. "dbsnp,clinvar,cadd.phred,gnomad_genome.af".
- `query` (string, required): rsID, HGVS id, or fielded query. e.g. "rs58991260", "chr1:g.218631822G>A", "dbnsfp.genename:CDK2".
- `size` (number): Max hits to return, 1-1000 (default 10).

### `variant` (~256 tokens)

Get the full merged annotation for a single human genetic variant by its HGVS id (e.g. "chr7:g.140453136A>T"). COORDINATES ARE hg19/GRCh37 BY DEFAULT — pass assembly "hg38" for GRCh38 positions, which is what gnomAD and Ensembl hand you. Returns annotations aggregated from dbSNP, ClinVar (pathogenicity / clinical significance), CADD and dbNSFP (deleteriousness/conservation scores), and gnomAD (population allele frequencies). Use to look up a known variant and read its pathogenicity and population frequency.

Input parameters:

- `assembly` (string): Genome build for the coordinates you pass AND the ids you get back: "hg19" (GRCh37, the default) or "hg38" (GRCh38). gnomAD and Ensembl coordinates are GRCh38.
- `fields` (string): Comma-separated return fields (default: all). e.g. "clinvar,gnomad_genome.af,cadd.phred".
- `id` (string, required): An HGVS variant id, e.g. "chr7:g.140453136A>T" (hg19 unless you set assembly).

### `metadata` (~48 tokens)

Returns MyVariant.info build metadata: total indexed variant count, available annotation sources (dbSNP, ClinVar, CADD, dbNSFP, gnomAD), and their current release/build versions.

## Diagnostics

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

## Score history

- 2026-11-05: 81
- 2026-11-04: 81
- 2026-11-03: 65
- 2026-11-02: 78
- 2026-11-01: 78
- 2026-10-31: 78
- 2026-10-30: 78
- 2026-10-29: 78

## Common questions

### What is the Myvariant MCP server?

Myvariant is an MCP server listed in the public MCP registry as io.github.pipeworx-io/myvariant. MyVariant.info MCP. Aggregated human genetic-variant annotation: dbSNP, ClinVar clinical… This page covers its npm package (@pipeworx/mcp-myvariant).

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

Myvariant scores 81 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 Myvariant MCP server expose?

Myvariant exposes 3 tools: query, variant, metadata. Their descriptions and schemas cost roughly 617 tokens of context every time the server is loaded.

### Is the Myvariant MCP server still maintained?

Myvariant 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 Myvariant MCP server under?

Myvariant 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 Myvariant MCP server?

VerifyMCP ran 16 checks on Myvariant, 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-myvariant
- Socket report: https://socket.dev/npm/package/@pipeworx/mcp-myvariant
- Repository: https://github.com/pipeworx-io/mcp-myvariant
- Website: https://pipeworx.io/packs/myvariant
- Changelog RSS feed: https://verifymcp.io/servers/pipeworx-io-myvariant/pipeworx-mcp-myvariant.xml
- Changelog JSON feed: https://verifymcp.io/servers/pipeworx-io-myvariant/pipeworx-mcp-myvariant/changelog.json
- Trust report (JSON): https://verifymcp.io/servers/pipeworx-io-myvariant/pipeworx-mcp-myvariant.json
- HTML version of this page: https://verifymcp.io/servers/pipeworx-io-myvariant/pipeworx-mcp-myvariant