Variant Annotation

Query and annotate gene variants from ClinVar and dbSNP databases. Trigger when: - User provides a variant identifier (rsID, HGVS notation, genomic coordinat...

This skill appears to be a legitimate variant-annotation tool that queries public NCBI endpoints (ClinVar and dbSNP). However, before installing or running it, consider the following: - Privacy: Variant strings and any patient-associated identifiers you pass to the tool will be sent to public databases (NCBI E-utilities). Do not feed identifiable patient data you cannot share publicly. - Implementation gaps: The SKILL.md promises population databases (gnomAD/ExAC/1000G) and functional predictors (SIFT, PolyPhen, CADD), but the manifest and requirements do not document how those are fetched. Review the full scripts/main.py to confirm which external APIs the code uses and whether additional API keys or local data files are required. - Missing dependency/install instructions: requirements.txt is minimal. If you plan to run the script, inspect main.py and run it in an isolated environment (virtualenv or container) to identify missing Python packages and avoid inadvertently executing unreviewed code system-wide. - Rate limits and API keys: The code supports an optional NCBI API key to increase rate limits. The skill does not declare how to supply that key; consider storing any API key securely and verify the CLI/argument behavior before providing secrets. - Security hygiene: Run the code on non-production data initially, review all network endpoints in the full source, and, if you need to use data that must remain private, evaluate running a local install of necessary databases or use tools that permit offline annotation. If you want, I can (a) scan the remainder of scripts/main.py for hidden endpoints or suspicious code, (b) list exact places where the implementation diverges from the SKILL.md, or (c) suggest a safe step-by-step to run the tool in a sandboxed environment.

Type: OpenClaw Skill Name: variant-annotation-2 Version: 0.1.0 The skill bundle is a legitimate bioinformatics tool designed to annotate genetic variants using NCBI's ClinVar and dbSNP databases. The core logic in `scripts/main.py` implements standard API interactions with NCBI E-utilities, including proper rate limiting and error handling, and follows the ACMG guidelines described in the documentation. There is no evidence of malicious intent, data exfiltration, or unauthorized execution; all network activity is directed toward official NCBI endpoints (eutils.ncbi.nlm.nih.gov).