Ncbi Variation MCP Server

@pipeworx/ncbi-variation

dbSNP refSNP records and HGVS ↔ SPDI ↔ rsID normalization from NCBI Variation Services — the service that turns any spelling of a human genetic variant into the canonical coordinates the rest of genomics keys on.

Part of Pipeworx — an MCP gateway connecting AI agents to 1865+ live data sources. This is an independent, unofficial integration — not affiliated with, endorsed by, or published by the upstream provider.

Tools

• variation_refsnp(rsid, assembly?, max_frequencies?) — the full refSNP record: genomic placement on the build you ask for, HGVS genomic/transcript/ protein forms, SPDI, gene context, ClinVar clinical significance, and population allele frequencies (gnomAD, ExAC, 1000 Genomes, TOPMED, ALFA). Answers "what is rs113488022".
• variation_hgvs_to_spdi(hgvs) — normalize an HGVS expression to contextual SPDI alleles, and validate that the HGVS is well-formed at all.
• variation_spdi_to_rsids(spdi) — the reverse: coordinate + alleles from a VCF or pipeline → the rsIDs other databases key on.

Auth

Keyless. NCBI asks unauthenticated clients to stay under ~3 requests/second; the pack sends an identifying User-Agent.

Data sources

• https://api.ncbi.nlm.nih.gov/variation/v0/refsnp/{rsid} — refSNP record.
• https://api.ncbi.nlm.nih.gov/variation/v0/hgvs/{expr}/contextuals — HGVS → SPDI.
• https://api.ncbi.nlm.nih.gov/variation/v0/spdi/{spdi}/rsids — SPDI → rsIDs.

Traps

GRCh37 vs GRCh38 is the whole game. One refSNP carries placements on both builds at different coordinates — rs113488022 (BRAF V600E) is 7:140753336 on GRCh38 and 7:140453136 on GRCh37, 300kb apart. A caller who takes a coordinate from one build into a dataset annotated on the other gets "not found", which reads as "this variant does not exist". So assembly is an explicit argument (default GRCh38), every response states assembly_requested and assemblies_available, and an assembly with no placement says so in assembly_note instead of coming back as an empty array.

SPDI is 0-based, HGVS is 1-based. NC_000007.14:140753335:A:T and NC_000007.14:g.140753336A>T are the same variant. The off-by-one is the most common reason variation_spdi_to_rsids returns nothing.

A retired rsID is not an error. dbSNP merges rsIDs; a merged one returns merged_snapshot_data with no primary_snapshot_data at all. The pack detects that and returns status: "merged" plus the rsID to re-query (rs3735962 → rs328), rather than an empty record.

Reference alleles are in the allele list. dbSNP lists the reference as an allele whose deleted_sequence equals its inserted_sequence. Filtering those out is what separates alternate_alleles from noise.

The raw record is huge. rs328 carries thousands of citations and dozens of placements. The pack summarizes and caps (max_frequencies, 25 citations) — counts are always reported alongside so a truncation is visible.

Quick Start

Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):

{
  "mcpServers": {
    "ncbi-variation": {
      "url": "https://gateway.pipeworx.io/ncbi-variation/mcp"
    }
  }
}

What this endpoint actually serves

tools/list at https://gateway.pipeworx.io/ncbi-variation/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 1865+ 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/variation_refsnp \
  -H 'Content-Type: application/json' \
  -d '{"rsid":"rs113488022","assembly":"GRCh38"}'

No account needed for the first calls. Inspect any tool: GET https://gateway.pipeworx.io/v1/tools/variation_refsnp. Find one: POST https://gateway.pipeworx.io/v1/tools/search_packs with {"query":"..."}.

Run it from npm

@pipeworx/mcp-ncbi-variation is a local stdio bridge to the Pipeworx gateway: your MCP client starts it with npx, and it forwards every call to the same https://gateway.pipeworx.io/ncbi-variation/mcp endpoint shown above. It needs network access; there is no offline mode.

{
  "mcpServers": {
    "ncbi-variation": {
      "command": "npx",
      "args": ["-y", "@pipeworx/mcp-ncbi-variation"]
    }
  }
}

Without a key it calls anonymously, capped at 50 calls a day. A free account raises that to 200 a day: get a key at https://pipeworx.io/signup and add "env": { "PIPEWORX_API_KEY": "<your key>" } to the server entry. The key is sent as a Bearer token, the same way a hosted connection sends it, so calls are metered and billed exactly as they are there.

It lists only this pack's tools by default. Set PIPEWORX_META_TOOLS=1 to also list ask_pipeworx and the other gateway-wide tools.

Behind an HTTPS proxy: Node's built-in fetch does not read HTTPS_PROXY by default. Newer Node releases honour it when NODE_USE_ENV_PROXY=1 is set; check your Node version's documentation.

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 Ncbi Variation data" })

The gateway picks the right tool and fills the arguments automatically.

More

• Docs and guides
• pipeworx.io

License

MIT