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Clarity Clinical

Query clinical variant data from ClinVar and gnomAD via Clarity Protocol. Use when the user asks about ClinVar classification, clinical significance, pathoge...

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Query clinical variant data from ClinVar and gnomAD via Clarity Protocol. Use when the user asks about ClinVar classification, clinical significance, pathoge...

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Requirements

Target platform: OpenClaw
Install method: Manual import
Extraction: Extract archive
Prerequisites: OpenClaw
Primary doc: SKILL.md

Package facts

Download mode: Yavira redirect
Package format: ZIP package
Source platform: Tencent SkillHub
What's included: SKILL.md, scripts/api_client.py, scripts/query_clinical.py

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Release facts

Source: Tencent SkillHub
Verification: Indexed source record
Version: 1.0.0

Provenance

Publisher: clarityprotocol
Source page: View original listing
Canonical URL: Open canonical page

Documentation

ClawHub primary doc Primary doc: SKILL.md 9 sections Open source page

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: python scripts/query_clinical.py Filter by gene symbol: python scripts/query_clinical.py --gene-symbol MAPT Get details for a specific variant: python scripts/query_clinical.py --gene MAPT --variant NM_005910.6:c.926C>T Get variant details in readable format: 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: export CLARITY_API_KEY=your_key_here python scripts/query_clinical.py --gene-symbol MAPT Get your API key at https://clarityprotocol.io

Error Handling

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.

Pagination

Clinical variant lists are paginated. The API returns a next_cursor field if more results are available.

Use Cases

Check if a variant is pathogenic in ClinVar Get population frequency data for a mutation Compare clinical significance across variants in a gene Assess variant review status quality Filter common vs. rare variants using gnomAD

Category context

Code helpers, APIs, CLIs, browser automation, testing, and developer operations.

Source: Tencent SkillHub

Largest current source with strong distribution and engagement signals.

Package contents

Included in package

2 Scripts1 Docs

SKILL.md Primary doc
scripts/api_client.py Scripts
scripts/query_clinical.py Scripts