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Get Started Free →clawbio/clinical-variant-prioritizer
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).
Passed 16 of 21 test cases with the skill, and 11 of 21 without it.
and 5 more in the full report
6 fixed11 passed either way5 still failing0 broke
Tokens, turns and time describe resource use, not a dollar price.
One of 6 test cases the skill fixed. Same model, same prompt, with and without the skill.
A patient file contains 100 loci, of which 80 match loci present in the active clinical panel. What summary field tracks the number of loci evaluated against the panel?
| Checked | Without skill | With skill |
|---|---|---|
| Reports loci_tested as the summary field for panel loci evaluated. | Missed | Passed |
The instructions your model reads when the skill loads.
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.
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.
from api import run
result = run(
{"rs28941785": "CT", "rs1800562": "GG"}, # rsid -> genotype
options={"panel_path": "..."}, # optional custom panel
)
test cases passed, vs 11 / 21 without
More skills from the same source and nearby in the registry, with their headline benchmark lift.