GeneBe — MCP server for Claude Code: human variant annotation
Lets your assistant look up genetic variants instead of guessing: ACMG classification with points, gnomAD frequencies, ClinVar. Research use only.
claude mcp add --transport http genebe-mcp https://mcp.genebe.net/v1/mcpWhat GeneBe does
GeneBe MCP answers questions about a single human variant from real data. You can hand it genomic coordinates, HGVS, an rsID or SPDI; hg19, hg38 and T2T are handled through liftover, and hg38 is the default build.
What comes back is auditable. The ACMG verdict carries points and a written reason for every criterion that applied, alongside gnomAD frequencies, in-silico predictor scores, ClinVar records, per-transcript consequences and a link to the GeneBe page. Long lists get capped, so a call lands around 1–3k tokens.
The server is remote, so there is nothing to install locally beyond its URL https://mcp.genebe.net/v1/mcp. No account and no API key. Access is read-only, and single variants only — no VCF files, no samples, no patient data. Classifications are for research; a qualified specialist has to review them before any clinical use, since this is not a medical device.
What it helps with
- check whether NM_005577.4:c.4195A>C is benign
- see why a variant got its ACMG classification
- convert rs41272110 to hg38 coordinates
- list a variant's consequences on every transcript
- pull gnomAD frequencies and ClinVar data for one variant
Example prompts for the agent
- Look up chr6-160585140-T-G and explain why it is classified that way
- Show me the LPA gene: identifiers, MANE Select, transcripts
How to install GeneBe
Platform CLI: remote server
claude mcp add --transport http genebe-mcp https://mcp.genebe.net/v1/mcpPlatform CLI: remote server
codex mcp add genebe --url https://mcp.genebe.net/v1/mcpConfig file
{
"mcpServers": {
"genebe": {
"url": "https://mcp.genebe.net/v1/mcp"
}
}
}Config file
{
"servers": {
"genebe": {
"type": "http",
"url": "https://mcp.genebe.net/v1/mcp"
}
}
}Platform CLI: remote server
gemini mcp add -t http genebe https://mcp.genebe.net/v1/mcpStep by step, with commands for each platform: How to add an MCP server to Claude Code, Codex, Cursor, VS Code, Gemini CLI and more
Questions about GeneBe
How do I install GeneBe in Claude Code?
Run claude mcp add --transport http genebe https://mcp.genebe.net/v1/mcp. No sign-up or API key is needed.
What does GeneBe MCP do?
It annotates and classifies human genetic variants, returning an ACMG verdict with points and criteria, gnomAD frequencies, predictor scores, ClinVar data and per-transcript consequences.
Can I use the classifications in clinical practice?
No. The server is marked research use only and is not a medical device or a diagnosis. A qualified specialist must review any classification.
