gnomAD
Integrates with gnomAD (Genome Aggregation Database) through ten specialized tools for querying genomic variant data, population frequencies, gene constraints, transcript analysis, and structural variants across multiple datasets and reference genomes for clinical genetics and population genomics research.
0Tools
8Findings
10Stars
Mar 22, 2026Last Scanned
2 critical · 4 high · 1 medium · 1 low findings detected
Security Category Deep Dive
Prompt Injection
Prompt & context manipulation attacks
69
Maturity
14
Rules
5
Sub-Categories
1
Gaps
64%
Implemented
56
Tests
1
Stories
100%3 rules
Injection via tool descriptions and parameter fields
GAP-001Prompt Injection Coverage GapMissing detection coverage for emerging prompt injection attack variants not addressed by current rules
100%4 rules
Hidden instructions via external content and tool responses
100%2 rules
Context window saturation and prior-approval exploitation
100%3 rules
Payload hiding via invisible chars, base64, schema fields
100%2 rules
Injection via prompt templates and runtime tool output
Findings8
2critical
4high
1medium
1low
Critical2
criticalC1Command InjectionMCP03-command-injectionAML.T0054
Pattern "`[^`]+`" matched in source_code: "`HTTP error! status: ${response.status}`" (at position 1404)
Replace exec()/execSync() with execFile() and pass arguments as an array, never as a string. Validate all inputs against an allowlist before use in any shell context. For subprocess.run, always pass a list and shell=False.
criticalQ13MCP Bridge Package Supply Chain AttackMCP10-supply-chainAML.T0054
Pattern "["']@modelcontextprotocol/sdk["']\s*:\s*["'](?:\^|~|\*|latest)" matched in source_code: ""@modelcontextprotocol/sdk": "^" (at position 21262)
MCP bridge packages (mcp-remote, mcp-proxy, @modelcontextprotocol/sdk, fastmcp) are high-value supply chain targets — CVE-2025-6514 (CVSS 9.6) in mcp-remote affected 437,000+ installs. Always pin exact versions (no ^ or ~ ranges). Use lockfiles (package-lock.json, pnpm-lock.yaml, uv.lock). Never run `npx mcp-remote` without version pinning. Verify package integrity with `npm audit` or `pip-audit` before deployment. Reference: CVE-2025-6514, OWASP ASI04.
High4
highK11Missing Server Integrity VerificationMCP10-supply-chainAML.T0054
Pattern "(connect|load|register|add)[_\s-]?(mcp|server|tool)(?!.*(?:verify|validate|checksum|hash|sign|cert|fingerprint|pin))" matched in source_code: "Register tool" (at position 8978)
Implement cryptographic verification for MCP server connections: (1) Pin server TLS certificates or public keys, (2) Verify server tool definition checksums against a known-good manifest, (3) Use package manager integrity checks (npm integrity, pip --require-hashes). The MCP spec recommends but doesn't yet mandate server signing — implement it proactively. Required by ISO 27001 A.8.24 and CoSAI MCP-T6.
highK13Unsanitized Tool OutputMCP02-tool-poisoningAML.T0054
Pattern "(?:query|execute|select|find).*(?:return|respond|result|rows|data)(?!.*(?:sanitize|escape|encode|map|filter|select|pick))" matched in source_code: "query GetVariant($variantId: String!, $datasetId: Data" (at position 2684)
Sanitize all external data before including in tool responses. Implement output encoding that neutralizes prompt injection patterns. Truncate excessively long content. Validate structure before passing database results. Apply the principle: treat all external data as untrusted, even in tool outputs. Required by CoSAI MCP-T4.
highK16Unbounded Recursion / Missing Depth LimitsMCP07-insecure-configAML.T0054
Pattern "(invoke|call|execute)[_\s-]?(?:tool|agent|self)(?!.*(?:depth|level|limit|max[_\s-]?(?:depth|recursi|iter|call)|count))" matched in source_code: "CallTool" (at position 192)
Add explicit depth/recursion limits to all recursive operations. Use iterative approaches where possible. Set maximum depth for directory walking (max_depth=10), tree traversal (max_level=20), and agent re-invocation (max_calls=5). Implement circuit breakers that halt after N iterations. Required by EU AI Act Art. 15 (robustness) and OWASP ASI08.
highD1Known CVEs in DependenciesMCP08-dependency-vuln
Dependency "@modelcontextprotocol/sdk@0.5.0" has known CVEs:
Update dependencies to versions that patch known CVEs. Run 'npm audit fix' or 'pip-audit' to identify and resolve vulnerable dependencies.
Medium1
mediumK17Missing Timeout or Circuit BreakerMCP07-insecure-configAML.T0054
Pattern "(?:fetch|axios|got|request|urllib|httpx|http\.get|http\.post)\s*\((?!.*(?:timeout|signal|AbortSignal|deadline|cancel))" matched in source_code: "Request(" (at position 1060)
Add timeouts to ALL external calls: HTTP requests (30s), database queries (10s), subprocess execution (60s), and MCP tool calls (30s). Implement circuit breakers that open after N consecutive failures (e.g., opossum, cockatiel). Use AbortSignal for cancellable operations. Required by EU AI Act Art. 15 and OWASP ASI08.
Low1
lowF4MCP Spec Non-ComplianceMCP07-insecure-config
Server fails MCP spec compliance checks: required:server_name; required:server_version; required:protocol_version; recommended:tool_descriptions; recommended:parameter_descriptions
Follow the MCP specification for server metadata. Include server name, version, and protocol version. Provide descriptions for all tools and parameters.