rare-disease-genetic-counseling

Plugin rare-disease-genetic-counseling from marketplace genetic-counseling-skills in muwenbo/genetic-counseling-skills. Commands read from the repo's manifest — 10 days ago.

Skills (10)

• classify-cnv

  Build a reviewable ACMG/ClinGen constitutional CNV classification proposal for a germline deletion or duplication. Use when given a chromosomal interval or CNV and asked to classify a loss/gain, apply the Riggs point metric, interpret section scores, handle hg19 liftover, or add phenotype, inheritan

• classify-sequence-variant

  Build a reviewable ACMG/AMP and applicable ClinGen VCEP classification proposal for a constitutional germline sequence variant. Use when given genomic coordinates, HGVS, a gene/protein change, rsID, or an imported variant and asked to classify, interpret pathogenicity, evaluate ACMG criteria, or app

• draft-counseling-summary

  Draft clinician-facing and optional patient-facing rare-disease germline genetic counseling summaries from reviewed case facts and interpretation proposals. Use when asked to summarize a positive, VUS, or negative result; explain inheritance or family implications; prepare counseling notes; communic

• draw-pedigree

  Create a reviewable clinical pedigree figure or validated PED/JSON file from user-supplied family-history facts. Use when asked to draw, chart, or diagram a pedigree or family tree; visualize inheritance or segregation across relatives; render affection status, carriers, deceased individuals, proban

• filter-variant-callset

  Filter a large, locally stored annotated germline WES/WGS callset (VCF, TSV/CSV, or Excel) into a reviewable variant shortlist using reviewer-approved criteria. Use when filtering a full annotated callset that has no external prioritization result, by frequency, consequence, gene panel, quality, and

• find-variant-literature

  Discover, retrieve, and extract claim-level literature evidence for a rare-disease germline variant, gene-disease pair, ACMG criterion, or CNV region. Use when asked to find papers, search PubMed, fetch known PMIDs, review functional or segregation evidence, count reported cases, investigate de novo

• interpret-negative-or-vus

  Interpret a completed negative or VUS rare-disease germline analysis by checking QC and assay blind spots, generating restrained phenotype-specific hypotheses, and prioritizing orthogonal confirmatory tests. Use when asked what WES/WGS/panel testing may have missed, why a case is negative, what to t

• prepare-rare-disease-case

  Structure English or Chinese rare-disease germline clinical narratives into reviewable findings, explicit negatives, suspected diagnoses, treatments, confounders, missing information, and candidate HPO terms. Use when preparing a case, extracting phenotypes, reviewing a referral note, normalizing cl

• rank-disease-candidates

  Rank and explain rare-disease candidates from reviewed HPO terms, explicitly absent findings, observed genes, and optionally annotated variants. Use for phenotype-only differential generation, variant-backed gene prioritization, reconciling phenotype and genotype rankings, or investigating why a can

• review-variant-table

  Inspect and normalize testing-company Excel, CSV, or TSV germline variant exports into a reviewable variant inventory. Use when a user uploads a laboratory variant table and wants to identify the data sheet or header, map Chinese or English columns, audit company annotations, verify table structure,

Subagents (1)

• rare-disease-genetic-counselor

  Review-centered decision support for rare-disease constitutional and germline genetic counseling. Use for structuring English or Chinese case narratives and HPO terms, reviewing laboratory variant tables and annotated callsets, ranking disease candidates, proposing sequence-variant and CNV classific

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