`variation_hgvs_to_spdi`

Pack: ncbi-variation · Endpoint: https://gateway.pipeworx.io/ncbi-variation/mcp

No MCP client? Call it directly: GET https://gateway.pipeworx.io/v1/tools/variation_hgvs_to_spdi for the schema, then POST the same URL with its arguments for the data.

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

Tool description as the model sees it

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 that dbSNP/ClinVar keys on, and for validating that an HGVS string is well-formed at all.

Parameters

Name	Type	Required	Description
`hgvs`	string	yes	HGVS expression on a RefSeq accession, e.g. “NC_000007.14:g.140753336A>T” or “NM_004333.6:c.1799T>A”.

Example call

Arguments

{
  "hgvs": "NC_000007.14:g.140753336A>T"
}

curl

curl -X POST https://gateway.pipeworx.io/ncbi-variation/mcp \
  -H 'Content-Type: application/json' \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/call","params":{"name":"variation_hgvs_to_spdi","arguments":{"hgvs":"NC_000007.14:g.140753336A>T"}}}'

TypeScript (@pipeworx/sdk)

import { Pipeworx } from '@pipeworx/sdk';
const pipeworx = new Pipeworx();

const result = await pipeworx.call('variation_hgvs_to_spdi', {
  "hgvs": "NC_000007.14:g.140753336A>T"
});

Connect

Add this to your MCP client config, or use one-click install buttons:

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

See Getting Started for client-specific install steps.

variation_hgvs_to_spdi