AI agents call clinvar_query_variant_significance to retrieve information from OrigeneMCP without modifying anything — typically the context-gathering step in research, monitoring, and reporting workflows, before the agent takes action elsewhere.
The tool appears to query ClinVar for variant significance information. This is a read-only operation against a public database with no modification, deletion, or execution of arbitrary code. No financial or destructive effects possible. Confidence is moderate (0.7) rather than high because the description is empty, but the naming convention and server context strongly suggest it is a data retrieval tool.
From the tool's definition Tool name includes 'query' and 'clinvar' (a public biomedical database). The sibling tools on this server (clinvar_find_single_mutation, clinvar_get_best_refseqid_by_sequence, clinvar_query_sequence_variants) are all retrieval operations.
Documented attack patterns abuse exactly the kind of access clinvar_query_variant_significance gives an agent:
PolicyLayer is an MCP gateway — it sits between your AI agents and OrigeneMCP, and nothing reaches the server without passing your rules. This is the rule we recommend for clinvar_query_variant_significance:
{
"version": "1",
"default": "deny",
"tools": {
"clinvar_query_variant_significance": {}
}
}clinvar_query_variant_significance is read-only, so it stays allowed — but everything else on the server is denied unless you say otherwise.
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clinvar_query_variant_significance. It is categorised as a Read tool in the OrigeneMCP MCP Server, which means it retrieves data without modifying state.
Register the Origene MCP server in PolicyLayer and add a rule for clinvar_query_variant_significance: 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 OrigeneMCP. Nothing to install.
clinvar_query_variant_significance 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 clinvar_query_variant_significance 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 clinvar_query_variant_significance. 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.
clinvar_query_variant_significance is provided by the Origene MCP server (gentel-lab/origenemcp). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.
Start from OrigeneMCP, add the rest of your stack, and see everything your agents can call. Then put policy on all of it.
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439 OrigeneMCP tools catalogued and risk-classified — across an index of 43,000+ MCP servers.