Annotate a genomic variant (chromosome, position, reference allele, alternate allele
AI agents call annotate_variant to retrieve information from OpenCRAVAT without modifying anything — typically the context-gathering step in research, monitoring, and reporting workflows, before the agent takes action elsewhere.
The tool queries and returns annotation information about a genomic variant. It takes input coordinates and alleles and returns data (genetic change, rsID, CAid, HGVS, protein change). This is a pure read/query operation with no writes, deletions, or external operations triggered.
From the tool's definition 'Annotate a genomic variant (chromosome, position, reference allele, alternate allele' - retrieves annotation data for a given variant with no side effects
Documented attack patterns abuse exactly the kind of access annotate_variant gives an agent:
PolicyLayer is an MCP gateway — it sits between your AI agents and OpenCRAVAT, and nothing reaches the server without passing your rules. This is the rule we recommend for annotate_variant:
{
"version": "1",
"default": "deny",
"tools": {
"annotate_variant": {}
}
}annotate_variant is read-only, so it stays allowed — but everything else on the server is denied unless you say otherwise.
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Annotate a genomic variant (chromosome, position, reference allele, alternate allele. It is categorised as a Read tool in the OpenCRAVAT MCP Server, which means it retrieves data without modifying state.
Register the OpenCRAVAT MCP server in PolicyLayer and add a rule for annotate_variant: 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 OpenCRAVAT. Nothing to install.
annotate_variant is a Read tool with low risk. Read-only tools are generally safe to allow by default.
Yes. Add a rate_limit block to the annotate_variant 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.
Set action: deny in the PolicyLayer policy for annotate_variant. 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.
annotate_variant is provided by the OpenCRAVAT MCP server (karchinlab/oc-mcp). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.
Start from OpenCRAVAT, add the rest of your stack, and see everything your agents can call. Then put policy on all of it.
Free to start. No card required.
7 OpenCRAVAT tools catalogued and risk-classified — across an index of 43,000+ MCP servers.