MCP server

Ncbi Variation

io.github.pipeworx-io/ncbi-variation

Checked 26 Oct 2026, 08:29 UTC · Connected to it and listed its tools

dbSNP refSNP records and HGVS/SPDI/rsID normalization for human genetic variants, from NCBI…

Working at last checkOfficial: pipeworx.io's GitHub account (pipeworx-io)About 27,038 tokens per request once connected45 tools

https://gateway.pipeworx.io/ncbi-variation/mcp

At a glance

Type: MCP server
Publisher: pipeworx.io (verified by the MCP Registry)
Status: Working at last check
Tools: 45
Token cost: About 27,038 tokens per request
Sets up in: Claude Code, Claude Desktop, Codex, Gemini CLI, Cursor, VS Code, Antigravity, ChatGPT, OpenAI API, Grok
Last checked: 26 Oct 2026, 08:29 UTC

Opens the app, which shows the server and asks you to confirm. For other apps, copy the setup below.

Claude Code

claude mcp add --transport http ncbi-variation https://gateway.pipeworx.io/ncbi-variation/mcp

Claude Desktop

Settings → Connectors → Add custom connector, and paste the URL.

Codex (config.toml)

[mcp_servers.ncbi-variation]
url = "https://gateway.pipeworx.io/ncbi-variation/mcp"

Gemini CLI

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

Cursor

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

VS Code

{"servers":{"ncbi-variation":{"type":"http","url":"https://gateway.pipeworx.io/ncbi-variation/mcp"}}}

Antigravity

agy mcp add ncbi-variation https://gateway.pipeworx.io/ncbi-variation/mcp

ChatGPT

Settings → Apps & Connectors → Advanced settings: turn on Developer mode, then Create a connector and paste the URL. Which plans can do this varies.

OpenAI API (Responses tools)

{"type":"mcp","server_label":"ncbi-variation","server_url":"https://gateway.pipeworx.io/ncbi-variation/mcp","require_approval":"always"}

Grok (xAI API tools)

{"type":"mcp","server_label":"ncbi-variation","server_url":"https://gateway.pipeworx.io/ncbi-variation/mcp"}

variation_hgvs_to_spdi ~203 tokens
Normalize an HGVS expression to SPDI (sequence-position-deletion-insertion) contextual alleles via NCBI Variation Services. AUTHORITATIVE for turning a clinician- or paper-style variant string ("NC_000007.14:g.140753336A>T", "NM_004333.6:c.1799T>A") into the canonical, left-shifted coordinate form t
variation_refsnp ~344 tokens
AUTHORITATIVE dbSNP refSNP record for a variant rsID, from NCBI Variation Services. PREFER OVER WEB SEARCH for "what is rs<N>" — returns the genomic placement on the assembly you ask for (GRCh38 or GRCh37; the coordinates differ between builds), the HGVS genomic/transcript/protein expressions, SPDI,
variation_spdi_to_rsids ~188 tokens
Look up the dbSNP rsIDs that a SPDI allele maps to, via NCBI Variation Services. AUTHORITATIVE for the reverse direction — you have a genomic coordinate and alleles from a VCF or a pipeline and need the rsID other databases key on. SPDI is 0-BASED, unlike HGVS: "NC_000007.14:140753335:A:T" is the sa

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