clarity-clinical

# Clarity Clinical Skill

Access clinical variant annotations from ClinVar and population frequency data from gnomAD through Clarity Protocol's integrated database.

## Quick Start

List all clinical variants:

```bash
python scripts/query_clinical.py
```

Filter by gene symbol:

```bash
python scripts/query_clinical.py --gene-symbol MAPT
```

Get details for a specific variant:

```bash
python scripts/query_clinical.py --gene MAPT --variant NM_005910.6:c.926C>T
```

Get variant details in readable format:

```bash
python scripts/query_clinical.py --gene MAPT --variant NM_005910.6:c.926C>T --format summary
```

## Clinical Variant Fields

Each clinical variant includes:

- `gene_symbol`: HGNC gene symbol
- `variant_notation`: Full HGVS notation (transcript-based)
- `clinvar_significance`: Clinical significance classification (e.g., "Pathogenic", "Benign")
- `clinvar_review_status`: Review status stars (e.g., "criteria provided, multiple submitters")
- `clinvar_last_evaluated`: Date of last ClinVar evaluation
- `gnomad_af`: Allele frequency in gnomAD (population prevalence)
- `gnomad_ac`: Allele count in gnomAD
- `gnomad_an`: Total allele number in gnomAD
- `fetched_at`: When this data was retrieved from ClinVar/gnomAD

## ClinVar Significance Values

- **Pathogenic**: Strong evidence for disease causation
- **Likely pathogenic**: Moderate evidence for disease causation
- **Benign**: Strong evidence of no disease causation
- **Likely benign**: Moderate evidence of no disease causation
- **Uncertain significance**: Insufficient evidence
- **Conflicting interpretations**: Disagreement among submitters

## gnomAD Frequency Interpretation

- **af < 0.0001**: Very rare (< 0.01%)
- **af < 0.001**: Rare (< 0.1%)
- **af < 0.01**: Uncommon (< 1%)
- **af >= 0.01**: Common (>= 1%)

## Rate Limits

- **Anonymous (no API key)**: 10 requests/minute
- **With API key**: 100 requests/minute

To use an API key, set the `CLARITY_API_KEY` environment variable:

```bash
export CLARITY_AP...