Alphagenome Single Variant Analysis
google-deepmind/science-skills
Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API.
Screen a genotype set (array or WGS-derived) against OMIM-morbid, ACMG-SF and Hereditary-Cancer gene panels and prioritise carried variants by ClinVar significance, gnomAD frequency, inheritance…
Install Clinical Variant Prioritizer
$ npx skills add ClawBio/ClawBio --skill clinical-variant-prioritizer -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install ClawBio/ClawBio clinical-variant-prioritizer --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/clinical-variant-prioritizer .claude/skills/clinical-variant-prioritizer && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "clinical-variant-prioritizer" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/clinical-variant-prioritizer into .claude/skills/clinical-variant-prioritizer/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "clinical-variant-prioritizer", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/ClawBio/ClawBio/tree/main/skills/clinical-variant-prioritizerType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add ClawBio/ClawBio --skill clinical-variant-prioritizer -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install ClawBio/ClawBio clinical-variant-prioritizer --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/clinical-variant-prioritizer .agents/skills/clinical-variant-prioritizer && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "clinical-variant-prioritizer" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/clinical-variant-prioritizer into .agents/skills/clinical-variant-prioritizer/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "clinical-variant-prioritizer", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add ClawBio/ClawBio --skill clinical-variant-prioritizer -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install ClawBio/ClawBio clinical-variant-prioritizer --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/clinical-variant-prioritizer .cursor/skills/clinical-variant-prioritizer && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "clinical-variant-prioritizer" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/clinical-variant-prioritizer into .cursor/skills/clinical-variant-prioritizer/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "clinical-variant-prioritizer", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/ClawBio/ClawBio.git --path skills/clinical-variant-prioritizer--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add ClawBio/ClawBio --skill clinical-variant-prioritizer -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install ClawBio/ClawBio clinical-variant-prioritizer --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/clinical-variant-prioritizer .gemini/skills/clinical-variant-prioritizer && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "clinical-variant-prioritizer" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/clinical-variant-prioritizer into .gemini/skills/clinical-variant-prioritizer/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "clinical-variant-prioritizer", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install ClawBio/ClawBio clinical-variant-prioritizerInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add ClawBio/ClawBio --skill clinical-variant-prioritizer -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/clinical-variant-prioritizer .github/skills/clinical-variant-prioritizer && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "clinical-variant-prioritizer" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/clinical-variant-prioritizer into .github/skills/clinical-variant-prioritizer/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "clinical-variant-prioritizer", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add ClawBio/ClawBio --skill clinical-variant-prioritizer -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install ClawBio/ClawBio clinical-variant-prioritizer --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/clinical-variant-prioritizer .opencode/skills/clinical-variant-prioritizer && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "clinical-variant-prioritizer" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/clinical-variant-prioritizer into .opencode/skills/clinical-variant-prioritizer/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "clinical-variant-prioritizer", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
clinical-variant-prioritizer- GitHub stars
- 1.2k
- Token cost
- ~962 tokens
- SKILL.md length
- 326 words
- Files
- 4
- Skills in repo
- 104
- Repo updated
- First seen
- Licence
- MIT
At a glance
Screen a genotype set (array or WGS-derived) against OMIM-morbid, ACMG-SF and Hereditary-Cancer gene panels and prioritise carried variants by ClinVar significance, gnomAD frequency, inheritance…
- Tasks that involve Bioinformatics
- SKILL.md covers Why it is not a raw ClinVar…, Interface, Panel and Limitations, plus 1 more section
- Runs Python scripts from its folder; calls python
What it does
Clinical Variant Prioritizer is an agent skill from ClawBio/ClawBio. Screen a genotype set (array or WGS-derived) against OMIM-morbid, ACMG-SF and Hereditary-Cancer gene panels and prioritise carried variants by ClinVar significance, gnomAD frequency, inheritance model and zygosity, following the pathogenicity-screening method of Corpas et al. 2021 (Whole Genome Interpretation for a Family of Five).
Its SKILL.md is about 960 tokens, which your agent loads only when the skill is triggered. The skill folder holds 4 other files (for example `api.py`, `prioritize.py` and `tests/test_api.py`).
It sits in Research & Science, covering Bioinformatics. The repository describes itself as: 🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free. The licence is MIT.
When your agent uses it
- Tasks that involve Bioinformatics
Example prompts
- “/clinical-variant-prioritizer”
Requirements
- Python 3
What it can do on your machine
Read from SKILL.md and the folder at commit dece754. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships script files (Python), which the agent can run.
Shell commands in SKILL.md call:
python
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Clinical Variant Prioritizer loads about 962 tokens when it runs. Until then it costs about 91 tokens; SKILL.md has 326 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
The full file from ClawBio/ClawBio at commit dece754, republished under its MIT licence (© ClawBio). 326 words, ~962 tokens.
Download SKILL.mdSave it as
.claude/skills/clinical-variant-prioritizer/SKILL.md (or your agent's skills folder). This skill also uses 3 other files; get the full folder from GitHub.- name
- clinical-variant-prioritizer
- description
- Screen a genotype set (array or WGS-derived) against OMIM-morbid, ACMG-SF and Hereditary-Cancer gene panels and prioritise carried variants by ClinVar significance, gnomAD frequency, inheritance model and zygosity, following the pathogenicity-screening method of Corpas et al. 2021 (Whole Genome Interpretation for a Family of Five).
- license
- MIT
- metadata.version
- 0.1.0
- metadata.author
- Manuel Corpas
- metadata.domain
- genomics
- metadata.reference
- Corpas M, Megy K, Mistry V, Metastasio A, Lehmann E. Whole Genome Interpretation for a Family of Five. Front Genet. 2021;12:535123…
- metadata.tags
- clinical-genomics, variant-prioritisation, clinvar, acmg, pathogenicity, carrier-screening
clinical-variant-prioritizer
Turn a genotype set into a prioritised list of clinically relevant variants, the way a clinical genome analyst would: screen catalogued disease-gene panels, then rank what is carried by how much it matters, not by how loud the raw ClinVar label is.
This skill implements the pathogenicity-screening stage of Whole Genome Interpretation for a Family of Five (Corpas et al., Front Genet 2021): variants are filtered through OMIM-morbid, ACMG-SF and Hereditary-Cancer panels, intersected with ClinVar significance and gnomAD population frequency, and classified by inheritance model and zygosity.
Why it is not a raw ClinVar lookup
A raw lookup reports a label. This skill reports actionability. The same "pathogenic" allele means very different things depending on context:
| Context | Category |
|---|---|
| Dominant / risk gene, allele carried | actionable |
| Recessive gene, homozygous | affected |
| Recessive gene, heterozygous | carrier (reproductive-risk only) |
| Uncertain / conflicting ClinVar | uncertain (flagged, not acted on) |
| Benign allele carried | benign |
| Variant not carried | reference |
A heterozygous carrier of a common, recessive, benign-spectrum allele is not an actionable finding, even when ClinVar shows "pathogenic" submissions. Saying so plainly is the point.
Interface
from api import run
result = run(
{"rs28941785": "CT", "rs1800562": "GG"}, # rsid -> genotype
options={"panel_path": "..."}, # optional custom panel
)run() returns:
summary:panel_size,loci_tested,loci_carried,reference,not_tested, and per-category counts (actionable,affected,carriers,uncertain,benign).findings: ranked list (highest priority first); each carries gene, HGVS, consequence, genotype, zygosity, ClinVar significance + review status, gnomAD frequency, condition, inheritance, panel membership, category and a plain-languagerationale.headline,method,disclaimer.
Panel
data/clinical_panel.json is a curated set of catalogued clinical loci, each
shipping its ClinVar significance, ClinVar review status, gnomAD frequency,
consequence, condition and inheritance model, so the screen is deterministic and
offline-reproducible (no per-call ClinVar/gnomAD/VEP network round-trips). Extend
it by adding entries; keys may be rsids or stable variant ids for WGS-only
variants not present on arrays.
Limitations
Array-based input covers only catalogued loci and misses most rare variants; a clean screen is not a clean genome. Heterozygous calls do not establish phase. Confirm any finding with an accredited clinical assay. Research and educational use only; not a clinical diagnosis.
Test
python -m pytest tests/ -q© ClawBio, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
SKILL.md and 3 other files in skills/clinical-variant-prioritizer of ClawBio/ClawBio.
- SKILL.md
- api.py
- prioritize.py
- tests/test_api.py
Open the folder on GitHubat commit dece754
Compare with similar skills
Clinical Variant Prioritizer next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Clinical Variant Prioritizer this skillClawBio/ClawBio | 1.2k | — | ~962 | Automated safety check: Pass | MIT | |
| Alphagenome Single Variant Analysisgoogle-deepmind/science-skills | 3.2k | 2 repos | ~3k | Automated safety check: Notes | Apache-2.0 | |
| 13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3.2k | Automated safety check: Pass | MIT | |
| Clinvar Databasegoogle-deepmind/science-skills | 3.2k | 2 repos | ~3.9k | Automated safety check: Notes | Apache-2.0 | |
| Metabolic Study Planneraiming-lab/AutoResearchClaw | 15k | — | ~1.9k | Automated safety check: Pass | MIT | |
| Dbsnp Databasegoogle-deepmind/science-skills | 3.2k | 2 repos | ~3.4k | Automated safety check: Notes | Apache-2.0 |
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Related
Categories
Questions about Clinical Variant Prioritizer
What does Clinical Variant Prioritizer do?
Screen a genotype set (array or WGS-derived) against OMIM-morbid, ACMG-SF and Hereditary-Cancer gene panels and prioritise carried variants by ClinVar significance, gnomAD frequency, inheritance…. Clinical Variant Prioritizer is an agent skill from ClawBio/ClawBio. Screen a genotype set (array or WGS-derived) against OMIM-morbid, ACMG-SF and Hereditary-Cancer gene panels and prioritise carried variants by ClinVar significance, gnomAD frequency, inheritance model and zygosity, following the pathogenicity-screening method of Corpas et al.
When should I use Clinical Variant Prioritizer?
Clinical Variant Prioritizer fits situations like: tasks that involve Bioinformatics.
How do I install Clinical Variant Prioritizer in Claude Code?
Run `npx skills add ClawBio/ClawBio --skill clinical-variant-prioritizer -a claude-code`. Or copy the skill folder (skills/clinical-variant-prioritizer in ClawBio/ClawBio) into .claude/skills/clinical-variant-prioritizer in your project. Claude Code loads it when a task matches its description.
How do I install Clinical Variant Prioritizer in Codex?
Run `npx skills add ClawBio/ClawBio --skill clinical-variant-prioritizer -a codex`. Or copy the skill folder (skills/clinical-variant-prioritizer in ClawBio/ClawBio) into .agents/skills/clinical-variant-prioritizer in your project. Codex loads it when a task matches its description.
Can I use Clinical Variant Prioritizer in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add ClawBio/ClawBio --skill clinical-variant-prioritizer -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/clinical-variant-prioritizer, .gemini/skills/clinical-variant-prioritizer, .github/skills/clinical-variant-prioritizer and .opencode/skills/clinical-variant-prioritizer in your project.
What does Clinical Variant Prioritizer need to run?
Going by SKILL.md and its folder, Clinical Variant Prioritizer needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.
Does Clinical Variant Prioritizer access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Clinical Variant Prioritizer safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Clinical Variant Prioritizer use?
Clinical Variant Prioritizer is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Clinical Variant Prioritizer use?
About 962 tokens (SKILL.md is roughly 3.8k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Clinical Variant Prioritizer?
Skills that share tags, products or a category with Clinical Variant Prioritizer: Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars), Clinvar Database (google-deepmind/science-skills, 3.2k stars) and Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Clinical Variant Prioritizer?
ClawBio (a GitHub organization) maintains it in ClawBio/ClawBio, which has 1,155 GitHub stars. The repository holds 104 skills in this directory. The repository was last updated on October 9, 2026.
Source: ClawBio/ClawBio on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.