get_structural_variants

THE RISK

Low Risk

Why get_structural_variants needs a policy

This tool queries and retrieves structural variant information from a read-only genetic database. There are no side effects, no data modification, no code execution, and no financial implications. The blast radius of misuse is minimal—an agent could retrieve genetic data it shouldn't have access to (privacy concern), but the tool itself performs only data retrieval, not modification or destruction.

From the tool's definition Tool name 'get_structural_variants' and description 'Get structural variants in a genomic region' indicate retrieval of existing genetic data with no modification, creation, or deletion of records.

Documented attack patterns abuse exactly the kind of access get_structural_variants gives an agent:

POLICY

How to control get_structural_variants

PolicyLayer is an MCP gateway — it sits between your AI agents and gnomAD MCP Server, and nothing reaches the server without passing your rules. This is the rule we recommend for get_structural_variants:

policy.json

{
  "version": "1",
  "default": "deny",
  "tools": {
    "get_structural_variants": {}
  }
}

get_structural_variants is read-only, so it stays allowed — but everything else on the server is denied unless you say otherwise.

Create a free account and register gnomAD MCP Server — nothing to install.
Add this policy — paste it, or build it visually.
Point your MCP client (Claude, Cursor, anything) at your gateway URL.

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EXPLORE

Related tools and policies

More gnomAD MCP Server tools

Read get_coverage Get coverage information for a gene Read get_gene Get detailed information about a gene including constraint scores Read get_mitochondrial_variants Get mitochondrial variants Read get_region_variants Get variants in a specific genomic region Read get_transcript Get information about a specific transcript Read get_variant Get detailed information about a specific variant Read get_variants_in_gene Get all variants in a specific gene Read search Search for genes, variants, or regions in gnomAD

All 9 gnomAD MCP Server tools →

Read tools on other servers

M-Team MCP Server get_torrent_detail YouTube MCP Server search_channel Android Forensics ADB MCP Server parse_browser_history 0xarchive web3_challenge

Go deeper

The MCP Attack Database → Documented attack patterns against MCP deployments — and the policies that stop them.
Data exfiltration → How read access becomes an exfiltration channel when chained with untrusted content.
MCP token cost → What connecting this server costs in context-window tokens on every request.
Rate Limiting MCP Tool Calls: A Practical Guide →
MCP Security: Why Prompt Guardrails Aren't Enough →

FAQ

Questions about get_structural_variants

What does the get_structural_variants tool do? +

Get structural variants in a genomic region. It is categorised as a Read tool in the gnomAD MCP Server MCP Server, which means it retrieves data without modifying state.

How do I enforce a policy on get_structural_variants? +

Register the gnomAD MCP Server MCP server in PolicyLayer and add a rule for get_structural_variants: allow, deny, rate-limit, or require approval. Point your MCP client at the PolicyLayer proxy URL and the rule is enforced on every call, before it reaches gnomAD MCP Server. Nothing to install.

What risk level is get_structural_variants? +

get_structural_variants is a Read tool with low risk. Read-only tools are generally safe to allow by default.

Can I rate-limit get_structural_variants? +

Yes. Add a rate_limit block to the get_structural_variants rule in your PolicyLayer policy. For example, setting max: 10 and window: 60 limits the tool to 10 calls per minute. Rate limits are tracked per agent session and reset automatically.

How do I block get_structural_variants completely? +

Set action: deny in the PolicyLayer policy for get_structural_variants. The AI agent will receive a policy violation error and cannot call the tool. You can also include a reason field to explain why the tool is blocked.

What MCP server provides get_structural_variants? +

get_structural_variants is provided by the gnomAD MCP Server MCP server (shukwong/gnomad-mcp-server). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.

Enforce policy on every gnomAD MCP Server tool call.

Start from gnomAD MCP Server, add the rest of your stack, and see everything your agents can call. Then put policy on all of it.

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