NCBI Variation

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

3tools
0msauth
free tier50 calls/day

Tools

variation_refsnp

The dbSNP record for an rsID: coordinates on GRCh38 or GRCh37, HGVS, ClinVar significance, and population allele frequencies.

No parameters required.

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variation_hgvs_to_spdi

Normalizes an HGVS variant string to canonical SPDI coordinates, and validates it, via NCBI Variation Services.

No parameters required.

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variation_spdi_to_rsids

Maps a SPDI genomic coordinate and alleles back to the dbSNP rsIDs, via NCBI Variation Services.

No parameters required.

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Test with curl

The gateway speaks JSON-RPC 2.0 over HTTP POST. You can test any pack directly from the terminal.

List available tools
bash
curl -X POST https://gateway.pipeworx.io/ncbi-variation/mcp \
  -H "Content-Type: application/json" \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/list"}'
Call a tool
bash
curl -X POST https://gateway.pipeworx.io/ncbi-variation/mcp \
  -H "Content-Type: application/json" \
  -d '{"jsonrpc":"2.0","id":2,"method":"tools/call","params":{"name":"variation_refsnp","arguments":{}}}'

Use with the SDK

Install @pipeworx/sdk to call tools from any TypeScript/Node project.

TypeScript
import { Pipeworx } from '@pipeworx/sdk';
const px = new Pipeworx();
const result = await px.call("variation_refsnp", {});
ask_pipeworx
// Or ask in plain English:
const answer = await px.ask("dbsnp refsnp records and hgvs/spdi/rsid normalization for human genetic variants, from ncbi variation services");