clarity-clinicalQuery clinical variant data from ClinVar and gnomAD via Clarity Protocol. Use when the user asks about ClinVar classification, clinical significance, pathoge...
Install via ClawdBot CLI:
clawdbot install clarityprotocol/clarity-clinicalAccess clinical variant annotations from ClinVar and population frequency data from gnomAD through Clarity Protocol's integrated database.
List all clinical variants:
python scripts/query_clinical.pyFilter by gene symbol:
python scripts/query_clinical.py --gene-symbol MAPTGet details for a specific variant:
python scripts/query_clinical.py --gene MAPT --variant NM_005910.6:c.926C>TGet variant details in readable format:
python scripts/query_clinical.py --gene MAPT --variant NM_005910.6:c.926C>T --format summaryEach clinical variant includes:
gene_symbol: HGNC gene symbolvariant_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 evaluationgnomad_af: Allele frequency in gnomAD (population prevalence)gnomad_ac: Allele count in gnomADgnomad_an: Total allele number in gnomADfetched_at: When this data was retrieved from ClinVar/gnomADTo use an API key, set the CLARITY_API_KEY environment variable:
export CLARITY_API_KEY=your_key_here
python scripts/query_clinical.py --gene-symbol MAPTGet your API key at https://clarityprotocol.io
404 Not Found: The specified gene/variant combination does not exist in the clinical database.
429 Rate Limit: You've exceeded the rate limit. The script will display how long to wait.
500 Server Error: The API server encountered an error. Try again later.
Timeout: The request took longer than 30 seconds.
Clinical variant lists are paginated. The API returns a next_cursor field if more results are available.
Generated Mar 1, 2026
Genetic counselors use this skill to quickly retrieve ClinVar classifications and gnomAD frequencies for variants identified in patient genetic tests. This helps in interpreting pathogenicity, assessing disease risk, and providing evidence-based recommendations during counseling sessions, improving diagnostic accuracy and patient understanding.
Researchers in biotech and pharmaceutical companies leverage the skill to analyze clinical significance and population frequencies of variants in genes of interest. This aids in identifying pathogenic mutations for drug target validation, assessing genetic factors in clinical trials, and prioritizing therapeutic interventions based on variant impact.
Clinical diagnostic labs integrate this skill into their workflows to automate the retrieval of ClinVar annotations and gnomAD data for variant reports. It streamlines the generation of comprehensive clinical reports, ensures up-to-date classification data, and reduces manual lookup time, enhancing lab efficiency and compliance.
Academic researchers and students in genetics use the skill to query clinical variant data for studies on disease associations, population genetics, or gene function. It facilitates data collection for publications, hypothesis testing, and educational projects by providing easy access to integrated ClinVar and gnomAD databases.
Health technology companies incorporate this skill into personalized medicine platforms to offer users insights into their genetic variants. It enables features like risk analysis based on ClinVar classifications and population frequency, supporting apps that provide personalized health recommendations and genetic insights.
Offer tiered API access with higher rate limits and premium features, such as bulk queries or advanced analytics, through subscription plans. Revenue is generated from monthly or annual fees paid by research institutions, labs, and companies requiring frequent data access, with pricing based on request volume.
Sell enterprise licenses to clinical diagnostic laboratories for integrating the skill into their internal systems. This includes custom support, enhanced data security, and compliance features, with revenue from one-time licensing fees or annual contracts tailored to lab size and usage needs.
Provide free access with a 10 requests/minute limit to attract individual users and small projects, while upselling API keys for 100 requests/minute to power users and businesses. Revenue comes from API key purchases, with additional income from consulting services or custom integrations for larger clients.
💬 Integration Tip
Set the CLARITY_API_KEY environment variable to increase rate limits from 10 to 100 requests per minute, and use pagination with the next_cursor field for handling large datasets efficiently.
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