# GeneBe (remote · mcp.genebe.net)

Annotate and classify human genetic variants with GeneBe (ACMG, gnomAD, ClinVar). Research use only.

- Trust score: 73/100 (medium)
- Change this week: +3
- Registry status: active
- Liveness: live
- Owner verified: no
- Last scored: 2026-11-05

## Components

- remote · `mcp.genebe.net`: 73/100 (this document), [markdown](https://verifymcp.io/servers/net-genebe-genebe-mcp/v1-mcp.md), [page](https://verifymcp.io/servers/net-genebe-genebe-mcp/v1-mcp)

## Channel facts

- Endpoint: `https://mcp.genebe.net/v1/mcp`
- Transports: `streamable-http`
- Auth: `none`
- Version: `0.1.0`

## Trust breakdown

How this component scores in each security and reliability category. Every signal is checked automatically against the live server, and we only credit what we can confirm. Scores are 0–100 per category. Scoring method: https://verifymcp.io/docs/scoring (what has changed: https://verifymcp.io/docs/scoring/changelog)

Scored 2026-11-05.

- **Endpoint Security**: 66/100
  - The endpoint's TLS certificate is valid, in date, and uses a strong key.
  - No authorisation is required to call this server. Every tool declares its destructiveHint and none is destructive, so open access doesn't expose one.
  - HTTPS enforcement could not be verified: the plaintext port answered with HTTP 404, which proves neither a plaintext path nor enforcement.
  - HSTS check failed: the Strict-Transport-Security header is absent.
  - DNSSEC is configured correctly; the domain's records validate against the full chain to the root.
- **Transport & Reachability**: 100/100
  - Verified streamable-http transport via a live MCP handshake.
- **Schema Quality & AI Usability**: 68/100
  - AI-judged instruction clarity (excellent).
  - Context-footprint check failed: tool/resource definitions use about 1124 tokens (~187/item across 6 items; 6 tools + 0 resources), over budget; trim descriptions and params.
  - Usage-examples check failed: none of the tools include examples.
- **Stability & Change Management**: 47/100
  - Stability observed for 14 of 30 days with no destabilising changes; credit accrues until the full window elapses.
- **Tool Coverage**: 100/100
  - 100% of tools have a non-trivial description (not blank, and not just the tool's name).
  - 100% of tool parameters carry a description.
  - Structured output schemas are declared (100% of tools); any adoption earns full credit.
- **Tool Safety**: 100/100
  - No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.
  - We read all 6 captured tool definition(s), and no name or description among them implies an irreversible operation.
  - An AI judge read all 7 captured unit(s) of tool text and found none that tries to manipulate the model reading it.
- **Capabilities**: 100/100
  - Implements a current MCP spec version (2026-07-28).

## Install

### How do I install the GeneBe MCP server?

GeneBe is a hosted endpoint at https://mcp.genebe.net/v1/mcp, so there is nothing to install locally. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.

### Claude

```bash
claude mcp add --transport http net-genebe-genebe-mcp 'https://mcp.genebe.net/v1/mcp'
```

### Cursor

```json
{
  "mcpServers": {
    "net-genebe-genebe-mcp": {
      "url": "https://mcp.genebe.net/v1/mcp"
    }
  }
}
```

### VS Code

```json
{
  "servers": {
    "net-genebe-genebe-mcp": {
      "type": "http",
      "url": "https://mcp.genebe.net/v1/mcp"
    }
  }
}
```

### Codex

```toml
[mcp_servers.net-genebe-genebe-mcp]
url = "https://mcp.genebe.net/v1/mcp"
```

### opencode

```json
{
  "$schema": "https://opencode.ai/config.json",
  "mcp": {
    "net-genebe-genebe-mcp": {
      "type": "remote",
      "url": "https://mcp.genebe.net/v1/mcp",
      "enabled": true
    }
  }
}
```

### OpenClaw

```bash
openclaw mcp add net-genebe-genebe-mcp --url 'https://mcp.genebe.net/v1/mcp' --transport streamable-http
```

### Hermes

```yaml
mcp_servers:
  net-genebe-genebe-mcp:
    url: "https://mcp.genebe.net/v1/mcp"
```

### Netclaw

```json
{
  "McpServers": {
    "net-genebe-genebe-mcp": {
      "Transport": "http",
      "Url": "https://mcp.genebe.net/v1/mcp"
    }
  }
}
```

### Vellum

```bash
assistant mcp add net-genebe-genebe-mcp -t streamable-http -u 'https://mcp.genebe.net/v1/mcp'
```

### Other

```json
{
  "mcpServers": {
    "net-genebe-genebe-mcp": {
      "type": "http",
      "url": "https://mcp.genebe.net/v1/mcp"
    }
  }
}
```

The mcpServers block is a cross-client convention. Remote transports vary, so check your client's docs.

## Changelog

Every change recorded for this component, newest first. Days that predate change tracking, or that we cannot explain, say so: "we were watching and nothing happened" and "we were not watching" are different claims.

### 2026-11-04 (score 73, +1)

No change was recorded against any check on this day. Stability & Change Management went from 40 to 43. That category is still filling its 30-day observation window: 12 days of observed history at the previous scan, 13 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-11-02 (score 72, +1)

No change was recorded against any check on this day. Stability & Change Management went from 33 to 37. That category is still filling its 30-day observation window: 10 days of observed history at the previous scan, 11 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-10-31 (score 71, +1)

- [functional] Server version: 0.1.0 → 0.1.1

### 2026-10-29 (score 70, +1)

No change was recorded against any check on this day. Stability & Change Management went from 20 to 23. That category is still filling its 30-day observation window: 6 days of observed history at the previous scan, 7 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-10-27 (score 69, +1)

No change was recorded against any check on this day. Stability & Change Management went from 13 to 17. That category is still filling its 30-day observation window: 4 days of observed history at the previous scan, 5 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-10-24 (score 68, +1)

No change was recorded against any check on this day. Stability & Change Management went from 3 to 7. That category is still filling its 30-day observation window: 1 days of observed history at the previous scan, 2 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-10-23 (score 67, 0)

- [functional improvement] Stability: unverified → 0.03

### 2026-10-22 (score 67)

First indexed and scored.

## MCP tools (6)

### `annotate_variant` (~230 tokens)

Annotate and classify one human genetic variant using GeneBe.

Start here for any question about a variant (what is it, is it pathogenic/benign, how common is it).
Returns the ACMG verdict with points and criteria, population frequency (gnomAD), predictor scores
(REVEL, AlphaMissense, SpliceAI, ...), ClinVar status, transcript consequences, and links to the
GeneBe page to cite. Research use only; not a diagnosis.

Input parameters:

- `gene_symbol`: Force this gene for the classification, e.g. TP53
- `genome` (string): Genome build of coordinate input. Ignored for HGVS/rsID.
- `transcript`: Force this transcript for the classification, e.g. NM_000546.6
- `variant` (string, required): The variant. Accepts 'chr-pos-ref-alt' (6-160585140-T-G), HGVS with transcript (NM_005577.4:c.4195A>C), rsID (rs41272110), SPDI, or 'GENE p.Thr1399Pro'.

Output parameters:

- `clinvar`
- `consequences` (array)
- `conservation` (object)
- `dbsnp`
- `disclaimer` (string)
- `frequency`
- `gene`
- `links`
- `scores`
- `summary`: Human-readable variant summary from GeneBe, when the backend provides one
- `total_consequences` (integer)
- `truncated` (boolean)
- `variant`
- `verdict`
- `warning`

### `explain_acmg_decision_path` (~205 tokens)

Explain step by step why each classification criterion did or did not apply to a variant.

Use after annotate_variant when the user asks "why was this classified that way?". Returns an
ASCII rendering of the decision tree with the evaluated conditions. By default it explains the
germline ACMG verdict that annotate_variant returns; the somatic trees 'oncogenicity' (2022) and
'acgs-uk-onco' (2025) can be requested explicitly. Research use only.

Input parameters:

- `genome` (string): Genome build of coordinate input.
- `tree` (string): Decision tree: 'germline' (default), 'oncogenicity' or 'acgs-uk-onco'.
- `variant` (string, required): The variant, in any notation accepted by annotate_variant.
- `version` (string): Tree version: germline 2019 (default), oncogenicity 2022, acgs-uk-onco 2025.

Output parameters:

- `disclaimer` (string)
- `text` (string): ASCII rendering of how each criterion was evaluated
- `tree` (string)
- `truncated` (boolean)
- `variant`
- `version` (string)

### `convert_variant` (~152 tokens)

Convert a variant written in any notation into normalized hg38 genomic coordinates.

Use when you only need the chr/pos/ref/alt of a variant (for example to translate HGVS or an rsID),
without annotation. Does not classify the variant; use annotate_variant for that.

Input parameters:

- `input_genome` (string): Genome build of positional input (hg19 input is lifted to hg38).
- `variant` (string, required): HGVS (NM_007294.4:c.3756_3759del), rsID (rs429358), SPDI (NC_000007.14:11324573:C:T), 'chr-pos-ref-alt', or 'GENE p.Thr1700Ile'.

Output parameters:

- `error`
- `input` (string)
- `variants` (array): Resolved hg38 coordinates (usually exactly one)

### `get_variant_effects` (~92 tokens)

List a variant's predicted molecular consequences on every overlapping transcript.

Returns per-transcript HGVS (c. and p.), consequence terms (e.g. missense_variant) and impact,
most severe and MANE Select transcripts first. Lightweight: no frequencies or classification.

Input parameters:

- `genome` (string): Genome build of coordinate input.
- `variant` (string, required): The variant, in any notation accepted by annotate_variant.

Output parameters:

- `effects` (array)
- `total_effects` (integer)
- `truncated` (boolean)
- `variant`

### `get_gene` (~115 tokens)

Look up a human gene: identifiers, location, MANE Select transcript, ClinGen gene-disease validity.

Use for questions about a gene rather than a specific variant. Transcripts are listed with
MANE Select first and capped; check total_transcripts.

Input parameters:

- `gene` (string, required): Gene symbol (BRCA1), alias, HGNC id (HGNC:1100), 'entrez:672' or Ensembl id (ENSG...).
- `include_transcripts` (boolean): Also list the gene's transcripts.

Output parameters:

- `alternative_hgnc_ids` (array)
- `chr`
- `end`
- `ensembl_id`
- `gene_disease_validity` (array)
- `hgnc_id`
- `link` (string)
- `mane_select_ensembl`
- `mane_select_refseq`
- `message`: Set when an alias matched several genes
- `name`
- `ncbi_id`
- `omim_id`
- `start`
- `symbol` (string)
- `total_gene_disease_entries` (integer)
- `total_transcripts` (integer)
- `transcripts` (array)
- `truncated` (boolean)
- `uniprot_id`

### `liftover_coordinate` (~164 tokens)

Convert a genomic position, interval or variant between genome builds (hg19, hg38, t2t).

Check `status`: RESOLVED means one result, AMBIGUOUS means several candidates, anything else
means it could not be mapped (see errors). For variants, ref/alt are rebuilt against the target
reference and warnings such as REF_MISMATCH may apply.

Input parameters:

- `from_genome` (string, required): Genome build of the input.
- `query` (string, required): A position ('chr8:141310715'), an interval ('chr8:141310715-141310716') or a variant ('chr2-23423-A-C', HGVS, rsID).
- `to_genome` (string, required): Genome build to convert to.

Output parameters:

- `candidates` (array)
- `errors` (array)
- `from_genome` (string)
- `input` (string)
- `status` (string): RESOLVED, AMBIGUOUS, UNRESOLVED, INVALID, NOT_RECOGNIZED or UNSUPPORTED
- `to_genome` (string)
- `warnings` (array)

## Diagnostics

Captured diagnostic sections: TLS, DNSSEC, Authorisation, Transports. The full working is on the page: https://verifymcp.io/servers/net-genebe-genebe-mcp/v1-mcp#diagnostics

## Score history

- 2026-11-05: 73
- 2026-11-04: 73
- 2026-11-03: 72
- 2026-11-02: 72
- 2026-11-01: 71
- 2026-10-31: 71
- 2026-10-30: 70
- 2026-10-29: 70
- 2026-10-28: 69
- 2026-10-27: 69
- 2026-10-26: 68
- 2026-10-25: 68
- 2026-10-24: 68
- 2026-10-23: 67
- 2026-10-22: 67

## Common questions

### What is the GeneBe MCP server?

GeneBe is an MCP server listed in the public MCP registry as net.genebe/genebe-mcp. Annotate and classify human genetic variants with GeneBe (ACMG, gnomAD, ClinVar). Research use only. This page covers its hosted endpoint (https://mcp.genebe.net/v1/mcp).

### Is the GeneBe MCP server safe to use?

GeneBe scores 73 out of 100 on VerifyMCP. That is a record of what we were able to check automatically, not an endorsement. The category breakdown on this page shows every signal behind the number, including the ones we could not confirm.

### What tools does the GeneBe MCP server expose?

GeneBe exposes 6 tools: annotate_variant, explain_acmg_decision_path, convert_variant, get_variant_effects, get_gene, liftover_coordinate. Their descriptions and schemas cost roughly 958 tokens of context every time the server is loaded.

### Does the GeneBe MCP server require authentication?

No. We connected to GeneBe without credentials and it answered, so anything it exposes is reachable by anyone who knows the address.

### Is the GeneBe MCP server still maintained?

GeneBe is still listed as active in the MCP registry. We last reached this channel on 5 November 2026. Those dates come from our own scans of the registry and the channel itself, not from anything the publisher announced.

## Links

- Remote endpoint: https://mcp.genebe.net/v1/mcp
- Repository: https://github.com/genebe-net/genebe-mcp
- Website: https://genebe.net/
- Changelog RSS feed: https://verifymcp.io/servers/net-genebe-genebe-mcp/v1-mcp.xml
- Changelog JSON feed: https://verifymcp.io/servers/net-genebe-genebe-mcp/v1-mcp.json
- HTML version of this page: https://verifymcp.io/servers/net-genebe-genebe-mcp/v1-mcp