# GeneBe

Lets your assistant look up genetic variants instead of guessing: ACMG classification with points, gnomAD frequencies, ClinVar. Research use only.

- MCP server · `type=mcp` · Claude Code, Codex, Cursor, GitHub Copilot, Windsurf (Devin Desktop), Cline, Zed, Gemini CLI
- Author: genebe-net
- License: MIT · policy=link-only · description only; the file stays with the author
- Source: https://github.com/genebe-net/genebe-mcp
- Updated: 2026-10-22
- HTML: https://affpapa.org/en/nevibecode/mcp/genebe

## What it 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.

## Requirements
- Remote server: `https://mcp.genebe.net/v1/mcp`

## Install

### Claude Code (native platform)

**Platform CLI: remote server**
```bash
claude mcp add --transport http genebe-mcp https://mcp.genebe.net/v1/mcp
```

### Codex

**Platform CLI: remote server**
```bash
codex mcp add genebe --url https://mcp.genebe.net/v1/mcp
```

### Cursor

**Config file**
File `.cursor/mcp.json`:
```json
{
    "mcpServers": {
        "genebe": {
            "url": "https://mcp.genebe.net/v1/mcp"
        }
    }
}
```

### GitHub Copilot

**Config file**
File `.vscode/mcp.json`:
```json
{
    "servers": {
        "genebe": {
            "type": "http",
            "url": "https://mcp.genebe.net/v1/mcp"
        }
    }
}
```

### Gemini CLI

**Platform CLI: remote server**
```bash
gemini mcp add -t http genebe https://mcp.genebe.net/v1/mcp
```

## When to use it
- 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
- Look up chr6-160585140-T-G and explain why it is classified that way
- Show me the LPA gene: identifiers, MANE Select, transcripts

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