# Variant
Use variant commands for compact annotation, source-backed interpretation context,
and optional predictive and population-genetics sections.
## Accepted variant identifiers
BioMCP supports multiple input forms:
- rsID: `rs113488022`
- HGVS genomic: `chr7:g.140453136A>T`
- gene-protein form: `BRAF V600E`
## Get a variant record
```bash
biomcp get variant rs113488022
biomcp get variant "chr7:g.140453136A>T"
biomcp get variant "BRAF V600E"
```
The default output favors concise, clinically relevant context first.
## Request variant sections
Prediction section:
```bash
biomcp get variant "BRAF V600E" predict
```
ClinVar-focused section:
```bash
biomcp get variant rs113488022 clinvar
```
Population section:
```bash
biomcp get variant "chr7:g.140453136A>T" population
```
CIViC section:
```bash
biomcp get variant "BRAF V600E" civic
```
GWAS section (trait associations from GWAS Catalog):
```bash
biomcp get variant rs7903146 gwas
```
Predictions (aggregated prediction scores):
```bash
biomcp get variant "BRAF V600E" predictions
```
Conservation (GERP, phyloP):
```bash
biomcp get variant rs113488022 conservation
```
COSMIC (somatic mutation data):
```bash
biomcp get variant "BRAF V600E" cosmic
```
CGI (Cancer Genome Interpreter annotations):
```bash
biomcp get variant "BRAF V600E" cgi
```
cBioPortal (frequency data):
```bash
biomcp get variant "BRAF V600E" cbioportal
```
All supported sections:
```bash
biomcp get variant rs113488022 all
```
## Helper commands
```bash
biomcp variant articles "BRAF V600E"
biomcp variant oncokb "BRAF V600E" # requires ONCOKB_TOKEN
```
## Search variants
By gene and protein change:
```bash
biomcp search variant -g BRAF --hgvsp V600E --limit 5
```
By significance:
```bash
biomcp search variant -g BRCA1 --significance pathogenic --limit 5
```
With population and score filters:
```bash
biomcp search variant -g BRCA1 --max-frequency 0.01 --min-cadd 20 --limit 5
```
## Search GWAS associations
By gene:
```bash
biomcp search gwas -g TCF7L2 --limit 10
```
By trait:
```bash
biomcp search gwas --trait "type 2 diabetes" --limit 10
```
Trait search uses GWAS Catalog trait endpoints first, then study-association fallback paths when needed.
## Optional enrichment
Variant base output may include cBioPortal enrichment when available.
OncoKB is accessed explicitly via `biomcp variant oncokb "<gene> <variant>"` and requires `ONCOKB_TOKEN`.
## Prediction requirements
Prediction sections may require `ALPHAGENOME_API_KEY` depending on source path.
Unsupported inputs are surfaced with explicit validation messages.
## JSON mode
```bash
biomcp --json get variant "BRAF V600E"
biomcp --json get variant rs7903146 gwas
biomcp --json search gwas --trait "type 2 diabetes"
```
## Related guides
- [How to annotate variants](../how-to/annotate-variants.md)
- [How to predict effects](../how-to/predict-effects.md)
- [Gene](gene.md)
- [Trial](trial.md)
