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 genuinely query ClinVar and dbSNP and compute ACMG-style scores, but the documentation advertises additional data sources (gnomAD, ExAC, 1000 Genomes) and functional predictors (SIFT, PolyPhen, CADD) that the code does not clearly fetch or compute. Before installing or relying on it: - Do not treat outputs as clinical-grade without independent validation; this is not a substitute for professional genetic interpretation. - Review scripts/main.py fully (the repo content appears truncated in places) to confirm which external APIs are actually called and how allele frequencies/predictions are derived. - If you need gnomAD or CADD results, verify that those APIs or local database files are integrated — otherwise the tool may produce incomplete annotations. - Keep sensitive genomic data private: batch/VCF uploads contain health information. Confirm the tool only sends queries to NCBI endpoints and that you are comfortable with that network traffic. - If you plan to provide an NCBI API key, supply it via a secure mechanism (not hard-coded). - Consider running the script on test cases from references/example-variants.md to confirm expected outputs and to detect any missing evidence sources or mismatches between documentation and behavior.

Type: OpenClaw Skill Name: variant-annotation Version: 1.0.0 The skill's core functionality is benign, designed for legitimate bioinformatics variant annotation. However, the `scripts/main.py` file contains a significant arbitrary file read/write vulnerability. The `main()` function directly uses `args.file` and `args.output` parameters with `open()` without any path sanitization or restriction, potentially allowing an attacker to read or write to arbitrary file paths on the host system if the execution environment is not sufficiently sandboxed. While `SKILL.md` mentions 'Output directory restricted to workspace' and 'Script execution in sandboxed environment' in its security checklist, the code itself does not enforce these restrictions, making it a vulnerability rather than malicious intent.