A sophisticated bioinformatics tool for querying and interpreting gene variant clinical significance from global databases like ClinVar and dbSNP.
Install & Download
1. ClawHub CLI
The fastest way to install a skill directly from the registry.
npx clawhub@latest install variant-annotation
2. Manual Installation
Copy the skill folder to one of these locations
~/.openclaw/skills/ <project>/skills/ Priority: Workspace > Local > Bundled
3. Prompt Installation
Copy this prompt to OpenClaw to install it automatically.
Help me install variant-annotation using Clawhub. If Clawhub is not installed, install it first (npm i -g clawhub).
Prefer to download?
Get the raw skill files in a ZIP archive.
What is Variant Annotation?
The Variant Annotation skill is a technical tool designed for genomic researchers and developers using Openclaw Skills to automate the interpretation of genetic mutations. It bridges the gap between raw genomic identifiers and actionable clinical insights by querying established databases and applying ACMG guideline-based pathogenicity assessments. This skill enables users to transform rsIDs, HGVS notations, or genomic coordinates into comprehensive reports that include clinical significance, functional predictions, and population allele frequencies.
Variant Annotation Use Cases
- Determining if a specific genetic mutation is pathogenic, benign, or of uncertain significance based on ClinVar records.
- Automating the ACMG guideline-based pathogenicity scoring for high-throughput variant screening.
- Retrieving population frequency data from gnomAD and 1000 Genomes to assess variant rarity.
- Converting and validating different genomic formats such as VCF-style coordinates into HGVS protein or cDNA notations.
- Performing functional impact analysis using computational tools like SIFT, PolyPhen2, and CADD.
How Variant Annotation Works
- The user provides a variant identifier, such as an rsID (rs80357410), HGVS notation, or genomic coordinates.
- The system validates and parses the input to ensure it meets bioinformatics nomenclature standards.
- It initiates network requests to NCBI E-utilities, Ensembl VEP, and other bioinformatics APIs to gather metadata.
- The tool applies internal logic to calculate ACMG classification scores based on 28 distinct evidence criteria.
- All gathered data points are synthesized into a structured JSON output containing clinical, population, and functional evidence.
Variant Annotation Setup
To integrate this capability into your environment for Openclaw Skills, install the necessary Python dependencies and configure your API keys for better performance.
# Install required Python libraries
pip install -r requirements.txt
# Set your NCBI API key to increase rate limits (Optional but Recommended)
export NCBI_API_KEY='your_api_key_here'
Variant Annotation Data Schema & Taxonomy
The skill generates a highly structured JSON response that organizes variant data into logical domains. This schema is optimized for both human reading and machine processing within Openclaw Skills workflows.
| Section | Fields Included |
|---|---|
| Identification | Variant ID, Gene Symbol, Chromosome, Position, HGVS notations |
| Clinical Status | ClinVar significance, ACMG classification, ACMG score, Review status |
| Disease Context | Disease names, MedGen IDs, Pathogenicity per disease |
| Frequency Data | gnomAD (exome/genome) and 1000 Genomes allele frequencies |
| Functional Impact | SIFT, PolyPhen2, CADD scores, Mutation Taster predictions |
| Summary | A natural language interpretation of the findings |
Variant Annotation Advanced Features
- Batch query support for processing entire files of variants in one execution.
- Programmatic Python API for direct integration into bioinformatics pipelines.
- Automated ACMG evidence scoring (PVS1, PS1-4, PM1-6, etc.) with configurable thresholds.
- Multi-source integration fetching data from NCBI, gnomAD, Ensembl, and CADD simultaneously.
- Robust error handling for complex HGVS notation parsing and API rate limit management.
SKILL.md
Loading
Related Openclaw Skills
Survival Analysis (Kaplan-Meier)
An advanced clinical and biological research tool for generating Kaplan-Meier survival curves and calculating critical statistical metrics through Openclaw Skills.
Peer Review Response Drafter
A specialized AI agent skill designed to help researchers draft polite, structured, and professional response letters to academic journal reviewers.
Journal Matchmaker
An automated recommendation engine that matches academic abstracts with high-impact journals.
GO/KEGG Enrichment Analysis
An automated bioinformatics pipeline for performing Gene Ontology and KEGG pathway enrichment analysis with professional visualizations and interpretation.
BMad Brainstorming Coach (Carson)
A high-energy AI facilitator designed to lead innovation workshops and systematic brainstorming using the improv-based YES AND methodology.
OpenClaw Market Financial Data
A comprehensive financial data skill providing real-time and historical market intelligence for stocks and cryptocurrency.
Featured*
