Myvariant
MyVariant.info MCP. Aggregated human genetic-variant annotation: dbSNP, ClinVar clinical…
Installation
Ajoutez ceci à la configuration MCP de votre client (Claude Desktop : claude_desktop_config.json ; Cursor : .cursor/mcp.json ; VS Code et les autres utilisent la même forme « mcpServers »).
claude mcp add --transport http myvariant 'https://gateway.pipeworx.io/myvariant/mcp'{
"mcpServers": {
"myvariant": {
"type": "http",
"url": "https://gateway.pipeworx.io/myvariant/mcp"
}
}
}Documentation
Tirée du README du projet sur GitHub, actualisée chaque semaine. Les liens ouvrent GitHub.
Sommaire
mcp-myvariant
MyVariant.info MCP. Aggregated human genetic-variant annotation: dbSNP, ClinVar clinical significance, CADD/dbNSFP deleteriousness scores, gnomAD allele frequencies. Keyless BioThings API (sibling of MyGene.info). Docs: https://docs.myvariant.info/en/latest/
Part of Pipeworx — an MCP gateway connecting AI agents to 1800+ live data sources. This is an independent, unofficial integration — not affiliated with, endorsed by, or published by the upstream provider.
Tools
| Tool | Description |
|---|---|
query | 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. |
variant | 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. |
metadata | Returns MyVariant.info build metadata: total indexed variant count, available annotation sources (dbSNP, ClinVar, CADD, dbNSFP, gnomAD), and their current release/build versions. |
Quick Start
Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):
{
"mcpServers": {
"myvariant": {
"url": "https://gateway.pipeworx.io/myvariant/mcp"
}
}
}What this endpoint actually serves
tools/list at https://gateway.pipeworx.io/myvariant/mcp returns the tools in the table
above plus the shared Pipeworx meta-tools — ask_pipeworx,
discover_tools, search_within, remember/recall and the rest of the
gateway-wide set. So the tool count you see is larger than this table: a
single-pack endpoint currently lists roughly 30 shared tools alongside the
pack's own. The connection's initialize response states its exact scope, and
is the authoritative answer for a given day.
This is deliberate, not multiplexing by accident. The meta-tools are what let a
scoped connection answer a question this pack does not cover — via
ask_pipeworx, which routes across the whole catalog — without you adding a
second MCP server. There is currently no way to mount a pack endpoint without
them; if the extra schemas cost you more context than the routing is worth,
connect to the full gateway once rather than to several pack endpoints.
Or connect to the full Pipeworx gateway to get every pack's tools listed directly, instead of just this one's:
{
"mcpServers": {
"pipeworx": {
"url": "https://gateway.pipeworx.io/mcp"
}
}
}Both URLs reach the same gateway and the same 1800+ data sources. The
only difference is which pack's tools are listed directly; ask_pipeworx
reaches all of them from either one.
No MCP client? Call it over HTTP
curl -X POST https://gateway.pipeworx.io/v1/tools/myvariant_query \
-H 'Content-Type: application/json' \
-d '{"query":"rs58991260"}'No account needed for the first calls. Inspect any tool: GET https://gateway.pipeworx.io/v1/tools/myvariant_query. Find one: POST https://gateway.pipeworx.io/v1/tools/search_packs with {"query":"..."}.
Standalone (no gateway account)
This package also runs as a local stdio MCP server — no Pipeworx account, no gateway round-trip:
{
"mcpServers": {
"myvariant": {
"command": "npx",
"args": ["-y", "@pipeworx/mcp-myvariant"]
}
}
}Or run it directly to confirm it starts:
npx -y @pipeworx/mcp-myvariantIt speaks MCP over stdin/stdout and answers initialize/tools/list/tools/call
for only this pack's tools — none of the shared meta-tools the gateway
connection above adds. Same source, same tools, no ask_pipeworx routing.
Using with ask_pipeworx
Instead of calling tools directly, you can ask questions in plain English — this works on the pack endpoint above as well as on the full gateway:
ask_pipeworx({ question: "your question about Myvariant data" })The gateway picks the right tool and fills the arguments automatically.
More
License
MIT
Questions fréquentes
Qu'est-ce que Myvariant ?
MyVariant.info MCP. Aggregated human genetic-variant annotation: dbSNP, ClinVar clinical…
Comment installer Myvariant ?
Il fonctionne comme serveur distant. Dans Claude Code : claude mcp add --transport http myvariant 'https://gateway.pipeworx.io/myvariant/mcp'. Pour les autres clients, collez la configuration JSON de cette page dans leurs réglages MCP.
Faut-il une clé API pour Myvariant ?
Son entrée au registre n'indique aucune clé ni secret obligatoire. Certaines fonctions peuvent tout de même demander un compte auprès du service auquel il se connecte.
Myvariant est-il open source ?
Oui. Son code est sur GitHub sous licence MIT.
Qui maintient Myvariant ?
Il est publié par pipeworx-io. AI.tn le référence sans le maintenir ni le recommander.
Issu du registre MCP officiel. Être listé n'est pas une recommandation : vérifiez le code et les permissions d'un serveur avant de lui donner accès à vos données.