allele-registry-mcp-server

MCP server wrapping the ClinGen Allele Registry (https://reg.clinicalgenome.org) — canonical allele identity for genetic variants. Resolves any HGVS / dbSNP / ClinVar / gnomAD reference to a stable ClinGen Allele Registry ID (CA#) and its cross-references, so a variant keeps one identity across genome builds and transcript versions.

Cloudflare Worker built on McpAgent (agents/mcp), REST + Code Mode via @bio-mcp/shared. Read endpoints only; no auth. Dev port 8905.

Why it exists

tmVar3's ~550 GB of chromosome-sharded SQLite exists to turn an HGVS string into a canonical allele. The Allele Registry does the same thing over a free public REST API — so we wrap the API instead of re-hosting the index. Every allele_registry_execute result carries a verifiable _meta.citation, and a CA# is a content-addressed allele identifier that drops straight into the fleet's attestation story.

Related MCP server: OpenCRAVAT

Tools (Code Mode)

• allele_registry_search — discover endpoints in the curated catalog

• allele_registry_execute — run JS against the API in a V8 isolate (api.get/api.post, searchSpec, no network/keys); results carry _meta.citation

• allele_registry_get_schema / allele_registry_query_data — inspect + SQL-query staged results

Develop

./scripts/dev-servers.sh allele-registry   # wrangler dev on :8905
pnpm --filter allele-registry-mcp-server run test

Upstream

• Base: https://reg.clinicalgenome.org — GET /allele?hgvs=…, GET /allele/{CAid}, resolution by dbSNP / ClinVar / gnomAD / MyVariantInfo.

• Source descriptor: ClinGen Allele Registry (ClinGen / NIH, freely available).