GeneBe

by genebe.net · remote · no sign-in to list tools · v0.1.0 · published by net.genebe

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

Changes · 3

Compare Registry entry

6 tools: 3 change things and 3 only read.

Scanned Oct 22, 2026

Deletes or cancels0Claude Code: deny
Can't be undone0Claude Code: ask
Changes things3Claude Code: ask: see these tools
Only reads3Claude Code: allow: see these tools

2 checks matched something in the tool definitions. No finding is not a safety guarantee. How the checks work.

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

Findings

Matches of fixed checks, with the text they matched.

2 warn

Warnconvert_variant
The server marks "convert_variant" read-only (readOnlyHint: true), and its own name, description or input give the class "write".
Matched text
annotations: {"readOnlyHint":true,"destructiveHint":false,"idempotentHint":true,"openWorldHint":true}; The name "convert_variant" says "convert": a word for a change.
What this check looks for
Warnliftover_coordinate
The server marks "liftover_coordinate" read-only (readOnlyHint: true), and its own name, description or input give the class "write".
Matched text
annotations: {"readOnlyHint":true,"destructiveHint":false,"idempotentHint":true,"openWorldHint":true}; The description's first verb is "convert": a word for a change.
What this check looks for

Tools

Open a tool for its reasons and full description. Descriptions are the publisher's own words, shown as they are.

6 tools

Changes things 3Creates or changes something that can be changed back.Claude Code: ask

annotate_variantAnnotate and classify one human genetic variant using GeneBe.Reads text others writeNo findings
Why it is in this group
- Nothing in its name or description says what it does, so it is counted as a write.
- The server marks it read-only (readOnlyHint: true), but an annotation never lowers a class.
What it can reach
- untrusted-inputThe server marks it openWorldHint: true: it reaches things outside the server's own data.
Description, as the server wrote it
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.
Annotations the server declares
- destructiveHint: false
- idempotentHint: true
- openWorldHint: true
- readOnlyHint: true
convert_variantConvert a variant written in any notation into normalized hg38 genomic coordinates.Reads text others write1 finding
Why it is in this group
- The name "convert_variant" says "convert": a word for a change.
- The server marks it read-only (readOnlyHint: true), but an annotation never lowers a class.
What it can reach
- untrusted-inputThe server marks it openWorldHint: true: it reaches things outside the server's own data.
Findings
- Warn
  The server marks "convert_variant" read-only (readOnlyHint: true), and its own name, description or input give the class "write".
  Matched text
  annotations: {"readOnlyHint":true,"destructiveHint":false,"idempotentHint":true,"openWorldHint":true}; The name "convert_variant" says "convert": a word for a change.
  What this check looks for
Description, as the server wrote it
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.
Annotations the server declares
- destructiveHint: false
- idempotentHint: true
- openWorldHint: true
- readOnlyHint: true
liftover_coordinateConvert a genomic position, interval or variant between genome builds (hg19, hg38, t2t).Reads text others write1 finding
Why it is in this group
- The description's first verb is "convert": a word for a change.
- The server marks it read-only (readOnlyHint: true), but an annotation never lowers a class.
What it can reach
- untrusted-inputThe server marks it openWorldHint: true: it reaches things outside the server's own data.
Findings
- Warn
  The server marks "liftover_coordinate" read-only (readOnlyHint: true), and its own name, description or input give the class "write".
  Matched text
  annotations: {"readOnlyHint":true,"destructiveHint":false,"idempotentHint":true,"openWorldHint":true}; The description's first verb is "convert": a word for a change.
  What this check looks for
Description, as the server wrote it
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.
Annotations the server declares
- destructiveHint: false
- idempotentHint: true
- openWorldHint: true
- readOnlyHint: true

Only reads 3Looks things up and changes nothing.Claude Code: allow

explain_acmg_decision_pathExplain step by step why each classification criterion did or did not apply to a variant.Reads text others writeNo findings
Why it is in this group
- The name "explain_acmg_decision_path" says "explain": a word for reading.
What it can reach
- untrusted-inputThe server marks it openWorldHint: true: it reaches things outside the server's own data.
Description, as the server wrote it
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.
Annotations the server declares
- destructiveHint: false
- idempotentHint: true
- openWorldHint: true
- readOnlyHint: true
get_geneLook up a human gene: identifiers, location, MANE Select transcript, ClinGen gene-disease validity.Reads text others writeNo findings
Why it is in this group
- The name "get_gene" says "get": a word for reading.
What it can reach
- untrusted-inputThe server marks it openWorldHint: true: it reaches things outside the server's own data.
Description, as the server wrote it
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.
Annotations the server declares
- destructiveHint: false
- idempotentHint: true
- openWorldHint: true
- readOnlyHint: true
get_variant_effectsList a variant's predicted molecular consequences on every overlapping transcript.Reads text others writeNo findings
Why it is in this group
- The name "get_variant_effects" says "get": a word for reading.
What it can reach
- untrusted-inputThe server marks it openWorldHint: true: it reaches things outside the server's own data.
Description, as the server wrote it
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.
Annotations the server declares
- destructiveHint: false
- idempotentHint: true
- openWorldHint: true
- readOnlyHint: true

This is not a safety rating, and no finding is not a safety guarantee. The groups and findings come from fixed checks of the tool definitions the server returned on the date shown, not from its code or what it does when called. How the checks work.

Exfil surface

Which tools read private data, which read text someone else can write, and which can send data out. One of each is a path a prompt injection can use.

No private-data, untrusted-input, outbound path in this server alone: no tool is tagged private-data or outbound.

Reads private data0: Reads files, mail, messages, databases, secrets, calendars or repositories.
Reads text others write6: Brings in text someone else can write: web pages, inbound email, messages, issues and comments.; annotate_variant
convert_variant
explain_acmg_decision_path
get_gene
get_variant_effects
liftover_coordinate
Can send data out0: Can carry data to people or systems: it sends, posts or publishes, or takes a recipient, channel or URL.

Other servers in the same agent add their own tools to these paths. Audit your whole setup to see them together.

Remote posture

What anyone on the internet sees at the remote endpoint: an anonymous initialize and tools/list, and the public OAuth metadata.

Looked at Oct 22, 2026, 15:10 UTC, unchanged since Oct 22, 2026. No credentials were sent and no tool was called. What is looked at.

Reachable: yes
HTTP status of an anonymous initialize: 200
tools/list served without credentials: yes
Tools that change things, listed without credentials: 3
Protocol version: 2025-06-18
WWW-Authenticate on 401: not observed
resource_metadata in WWW-Authenticate: none
RFC 9728 protected resource metadata: none
Authorization servers: none
Legacy HTTP+SSE transport: no
Dynamic client registration: not observed
Client ID metadata documents: not observed

WarnThe whole server
The endpoint served tools/list without credentials, and the list has 3 tools that change things (3 write). Whether a call also works without credentials was not tested: tools are never called.
Matched text
https://mcp.genebe.net/v1/mcp: tools/list returned 6 tools to an anonymous client, including annotate_variant (write), convert_variant (write), liftover_coordinate (write)
What this check looks for

Install

Pinned to version 0.1.0. Values in angle brackets are yours to fill in.

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

Run in a terminal.

Claude Code permissions

Allow the reads, ask before a change or a way out, deny the deletes. Paste into .claude/settings.json.

.claude/settings.json

{
  "permissions": {
    "allow": [
      "mcp__genebe__explain_acmg_decision_path",
      "mcp__genebe__get_variant_effects",
      "mcp__genebe__get_gene"
    ],
    "ask": [
      "mcp__genebe__annotate_variant",
      "mcp__genebe__convert_variant",
      "mcp__genebe__liftover_coordinate"
    ],
    "deny": []
  }
}

Tools that only read are allowed, tools that change things ask first, tools that delete or cancel are denied. A read that can send data out (it takes a URL, say) asks first too. It assumes the server is installed as genebe. Review it before you use it.

Capability tags behind 6 rules

mcp__genebe__annotate_variant untrusted-input
mcp__genebe__explain_acmg_decision_path untrusted-input
mcp__genebe__convert_variant untrusted-input
mcp__genebe__get_variant_effects untrusted-input
mcp__genebe__get_gene untrusted-input
mcp__genebe__liftover_coordinate untrusted-input

Keep track

Get told when this server's tools change: a new tool, a new description, a new class.

https://anlyon.dev/servers/net.genebe/genebe-mcp/changes.xml

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Anlyon alternative

3 of these tools change something. Run those as governed actions.

Declare what an action changes, and Anlyon puts it under a shared limit, binds every approval to the exact request, and grades the outcome. It works on any HTTPS API you can describe as an action.

Anlyon does not run, proxy or govern this MCP server. A tool your own code calls directly is not routed through Anlyon and is not governed by it.

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Source: MCP Registry · repository. Synced Oct 22, 2026, 13:18 UTC.

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