variant-annotation
Query and annotate gene variants from ClinVar and dbSNP databases. Trigger when: - User provides a variant identifier (rsID, HGVS notation, genomic coordinates) and asks about clinical significance - User mentions "ClinVar", "dbSNP", "variant annotation", "pathogenicity", "clinical significance" - User wants to know if a mutation is pathogenic, benign, or of uncertain significance - User provides VCF content or variant data requiring interpretation - Input: variant ID (rs12345), HGVS notation (NM_007294.3:c.5096G>A), or genomic coordinates (chr17:43094692:G>A) - Output: clinical significance, ACMG classification, allele frequency, disease associations
Install via CLI (Recommended)
clawhub install openclaw/skills/skills/aipoch-ai/variant-annotationVariant Annotation
Query and interpret gene variant clinical significance from ClinVar and dbSNP databases with ACMG guideline support.
Purpose
Provide comprehensive variant annotation including:
- Clinical significance classification (Pathogenic, Likely Pathogenic, VUS, Likely Benign, Benign)
- ACMG guideline-based pathogenicity assessment
- Population allele frequencies (gnomAD, ExAC, 1000 Genomes)
- Disease and phenotype associations
- Functional predictions (SIFT, PolyPhen, CADD)
Supported Input Formats
| Format | Example | Description |
|---|---|---|
| rsID | rs80357410 | dbSNP reference SNP ID |
| HGVS cDNA | NM_007294.3:c.5096G>A | Coding DNA change |
| HGVS Protein | NP_009225.1:p.Arg1699Gln | Protein change |
| HGVS Genomic | NC_000017.11:g.43094692G>A | Genomic coordinate |
| VCF-style | chr17:43094692:G>A | Chromosome:position:ref>alt |
| Gene:AA | BRCA1:R1699Q | Gene with amino acid change |
Usage
Python API
from scripts.main import VariantAnnotator
# Initialize annotator
annotator = VariantAnnotator()
# Query by rsID
result = annotator.query_variant("rs80357410")
# Query by HGVS notation
result = annotator.query_variant("NM_007294.3:c.5096G>A")
# Query by genomic coordinate
result = annotator.query_variant("chr17:43094692:G>A")
# Batch query
results = annotator.batch_query(["rs80357410", "rs28897696", "rs11571658"])
Command Line
# Single variant query
python scripts/main.py --variant rs80357410
# HGVS notation
python scripts/main.py --variant "NM_007294.3:c.5096G>A"
# Genomic coordinate
python scripts/main.py --variant "chr17:43094692:G>A"
# Batch from file
python scripts/main.py --file variants.txt --output results.json
# With output format
python scripts/main.py --variant rs80357410 --format json
Output Format
Metadata
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Find the right skillPaste this into your clawhub.json to enable this plugin.
{
"plugins": {
"official-aipoch-ai-variant-annotation": {
"enabled": true,
"auto_update": true
}
}
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