Click on "Deploy Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type @ followed by the MCP server name and your instructions, e.g., "@allele-registry-mcp-server resolve HGVS NM_000546.5:c.100G>A to a CA ID"
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
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.
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
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
./scripts/dev-servers.sh allele-registry # wrangler dev on :8905
pnpm --filter allele-registry-mcp-server run testBase: 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).
This server cannot be deployed
Broad Institute gnomAD genomic variant database (GraphQL)
Look up allele frequencies by ancestry, gene constraint, variants, and coverage over gnomAD.
MCP gateway federating 22 biomedical MCP servers behind one endpoint: gnomAD, ClinVar, HPO, VEP.
Search and resolve Naturepedia, Robbie's Razor, and GC-MRD-v2.0 canonical resources.
