Skills clinvar-database
📦
clinvar-database
Content revision r1 Safe ⚙️ External commands🌐 Network access🔑 Env variables
Query ClinVar Variant Evidence
ClinVar data is large, versioned, and difficult to interpret safely. This skill guides Claude, Codex, and Claude Code through ClinVar searches, evidence review, and variant annotation workflows.
Supports: Claude Codex Code(CC)
Install with my Agent
Copy this request to your Agent. It includes the canonical Skill page and manifest.
Agent request
Review the Skillstore skill "clinvar-database" from https://skillstore.io/skills/davila7-clinvar-database.md and its manifest at https://skillstore.io/api/skills/davila7-clinvar-database/manifest. Verify the artifact. You may proceed after verification, subject to the environment's own policy.Your Agent should still show its plan and request any confirmation required by the security policy.
Agent-readable resources
Use these links when an AI agent, crawler, or script needs clean context instead of reading the full page.
Test it
Using "clinvar-database". Find high-confidence pathogenic CFTR variants.
Expected outcome:
A ranked summary of CFTR variants with pathogenic classifications, review status, condition names, and warnings for conflicts.
Using "clinvar-database". Explain a ClinVar VUS result.
Expected outcome:
A plain-language explanation that uncertain significance is not diagnostic and requires expert review with updated evidence.
Using "clinvar-database". Choose a format for a local ClinVar database.
Expected outcome:
A recommendation comparing XML, VCF, and tab-delimited files by completeness, pipeline fit, and maintenance cost.
Security Audit
Safev15 • 7/9/2026 Open versioned report
Confirmed risks are limited to an unsafe FTP pipe-to-shell installer and repeated FTP download guidance for ClinVar data. Official HTTPS URLs, Markdown backticks, placeholder API key text, and benign documentation examples were false positives. No evidence found of prompt injection, credential exfiltration, or malicious intent.
4
Files scanned
1,163
Lines analyzed
11
Review items
0
False positives ignored
Capability review items (11)
These are real local capabilities that may be expected for this skill, so they require review but are not counted as confirmed malicious behavior.
High
Shell command substitution
sh -c "$(curl -fsSL ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)"
The documentation recommends executing an installer fetched over FTP with sh. This creates a real remote code execution and tampering risk if followed by an agent or user.
High
FTP protocol
sh -c "$(curl -fsSL ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)"
The documentation recommends executing an installer fetched over FTP with sh. This creates a real remote code execution and tampering risk if followed by an agent or user.
Medium
FTP protocol
ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/
The skill recommends ClinVar bulk downloads over FTP. The source is public NCBI data, but FTP lacks transport encryption and integrity protection for downloaded datasets.
Medium
FTP protocol
BASE_URL="ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/clinvar_variation"
The skill recommends ClinVar bulk downloads over FTP. The source is public NCBI data, but FTP lacks transport encryption and integrity protection for downloaded datasets.
Medium
FTP protocol
FTP_BASE="ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar"
The skill recommends ClinVar bulk downloads over FTP. The source is public NCBI data, but FTP lacks transport encryption and integrity protection for downloaded datasets.
Medium
FTP protocol
Download complete datasets from `ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/`
The skill recommends ClinVar bulk downloads over FTP. The source is public NCBI data, but FTP lacks transport encryption and integrity protection for downloaded datasets.
Medium
FTP protocol
wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/clinvar_variation/ClinVarVariationRelease_00-latest.
The skill recommends ClinVar bulk downloads over FTP. The source is public NCBI data, but FTP lacks transport encryption and integrity protection for downloaded datasets.
Medium
FTP protocol
wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz
The skill recommends ClinVar bulk downloads over FTP. The source is public NCBI data, but FTP lacks transport encryption and integrity protection for downloaded datasets.
Medium
FTP protocol
wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz
The skill recommends ClinVar bulk downloads over FTP. The source is public NCBI data, but FTP lacks transport encryption and integrity protection for downloaded datasets.
Medium
FTP protocol
wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz.tbi
The skill recommends ClinVar bulk downloads over FTP. The source is public NCBI data, but FTP lacks transport encryption and integrity protection for downloaded datasets.
Medium
FTP protocol
wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/clinvar_variation/ClinVarVariationRelease_YYYY-MM.xm
The skill recommends ClinVar bulk downloads over FTP. The source is public NCBI data, but FTP lacks transport encryption and integrity protection for downloaded datasets.
Risk Factors
⚙️ External commands (50)
references/api_reference.md:138 references/data_formats.md:325-327 references/data_formats.md:319 references/data_formats.md:336 SKILL.md:33 SKILL.md:34 SKILL.md:35 SKILL.md:36 SKILL.md:37 SKILL.md:38 SKILL.md:42 SKILL.md:49-52 SKILL.md:52-58 SKILL.md:58-64 SKILL.md:64-90 SKILL.md:90-92 SKILL.md:92-101 SKILL.md:101-102 SKILL.md:102-106 SKILL.md:106-107 SKILL.md:107-111 SKILL.md:111-112 SKILL.md:112-113 SKILL.md:113-116 SKILL.md:116-122 SKILL.md:122-131 SKILL.md:131-141 SKILL.md:141-148 SKILL.md:148-157 SKILL.md:157-160 SKILL.md:160-169 SKILL.md:169-176 SKILL.md:176-190 SKILL.md:190-193 SKILL.md:193-198 SKILL.md:198-213 SKILL.md:213-215 SKILL.md:215-239 SKILL.md:239-257 SKILL.md:257-259 SKILL.md:259-270 SKILL.md:270-273 SKILL.md:273-275 SKILL.md:275-280 SKILL.md:280-282 SKILL.md:282-284 SKILL.md:284-292 SKILL.md:292-294 SKILL.md:294-306 SKILL.md:306-308
🌐 Network access (29)
references/api_reference.md:15 references/api_reference.md:25 references/api_reference.md:38 references/api_reference.md:54 references/api_reference.md:66 references/api_reference.md:84 references/api_reference.md:95 references/api_reference.md:103 references/api_reference.md:115 references/api_reference.md:122 references/api_reference.md:128 references/api_reference.md:131 references/api_reference.md:138 references/data_formats.md:11 references/data_formats.md:322 references/data_formats.md:339 SKILL.md:30 SKILL.md:51 SKILL.md:238 SKILL.md:348 SKILL.md:349 SKILL.md:350 SKILL.md:352 SKILL.md:90 SKILL.md:118 SKILL.md:121 SKILL.md:271 SKILL.md:272 SKILL.md:307
🔑 Env variables (1)
Audited by: codex View Audit History →
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APA citation
davila7. (2026). clinvar-database security audit report (audit version 15) [Author version unspecified]. Skillstore. https://skillstore.io/skills/davila7-clinvar-database/audits/15BibTeX citation
@techreport{davila7-davila7-clinvar-database-2026,
author = {davila7},
title = {clinvar-database security audit report (audit version 15)},
institution = {Skillstore},
year = {2026},
number = {15},
url = {https://skillstore.io/skills/davila7-clinvar-database/audits/15},
note = {Author version unspecified}
}CITATION.cff
cff-version: 1.2.0
message: "If you use this Skill, cite its author and this versioned security audit report."
title: "clinvar-database security audit report (audit version 15)"
version: "unspecified"
type: report
authors:
- name: "davila7"
date-released: "2026-07-09"
url: "https://skillstore.io/skills/davila7-clinvar-database/audits/15"
identifiers:
- type: other
value: "skillstore:davila7-clinvar-database:audit:15"
description: "Skillstore immutable audit report identifier"
Compare variants
2 installable variantsEach author remains a separate installable skill. The recommended variant is ranked by Skillstore evidence.
Why this variant is first
Highest Skillstore Score
Author / source Skillstore Score Evidence Confidence Skillstore usage Updated
davila7-clinvar-database
Skillstore Score 75
Evidence Confidence High
Skillstore usage 7
Updated
2026-08-21
k-dense-ai-clinvar-database
Skillstore Score 69
Evidence Confidence High
Skillstore usage 11
Updated
2026-08-21
Skillstore Score
Why this score Evidence Confidence: High 45
Architecture
85
Maintainability
87
Content
74
Community
83
Spec Compliance
What You Can Build
Prioritize Variants for Review
Find variants in a gene and rank them by clinical significance and review status.
Annotate Sequencing Results
Plan a ClinVar VCF annotation workflow for a variant call set.
Build a Local Reference Dataset
Select ClinVar bulk formats and document update handling for a local database.
Try These Prompts
Search a Gene
Find ClinVar records for BRCA1 pathogenic variants. Summarize clinical significance, review status, and key cautions.
Review a Variant
Look up this HGVS variant in ClinVar. Explain the classification, review stars, conflicts, and why manual review is needed.
Plan VCF Annotation
Design a workflow to annotate my GRCh38 VCF with ClinVar. Include data format choice, version tracking, and validation checks.
Design a ClinVar Mirror
Propose a reproducible local ClinVar database design. Cover bulk formats, indexing fields, monthly updates, and conflict handling.
Best Practices
- Record the ClinVar release date and genome build for every analysis.
- Prefer expert panel or practice guideline classifications when available.
- Flag conflicts and VUS classifications for manual genetics review.
Avoid
- Do not treat ClinVar classifications as standalone clinical diagnoses.
- Do not mix GRCh37 and GRCh38 coordinates without explicit liftover checks.
- Do not ignore review status, submission age, or conflicting interpretations.
Frequently Asked Questions
Can this skill diagnose a patient?
No. It supports research and review workflows, but clinical decisions require qualified genetics professionals.
Which ClinVar formats does it cover?
It covers XML, VCF, and tab-delimited files, with guidance on when each format fits best.
Does it support API access?
Yes. It documents NCBI E-utilities operations for searching, summaries, full records, and related links.
How should conflicts be handled?
Conflicting interpretations should be flagged, reviewed against evidence, and evaluated by domain experts.
Can it annotate VCF files?
It provides workflow guidance for ClinVar VCF annotation and filtering with common bioinformatics tools.
Why track ClinVar versions?
Variant classifications can change, so release dates and access dates are needed for reproducible results.
Developer Details
Author
davila7License
MIT
Skillstore revision
r1
Version notice
The author did not declare a version.
Ref
b959ebfd1043a07c0c4378ab94ca4342cb0259f5
Maintenance freshness
7/20/2026
Usage
4 downloads · 474 views
File structure