Initial commit

configs/acmg_config.example.yaml

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+# ACMG evidence thresholds (example, adjust per lab policy)
+ba1_af: 0.05   # Stand-alone benign if AF >= this
+bs1_af: 0.01   # Strong benign if AF >= this (and not meeting BA1)
+pm2_af: 0.0005 # Moderate pathogenic if AF <= this
+bp7_splice_ai_max: 0.1 # Supporting benign if synonymous and predicted low splice impact
+
+# Genes considered loss-of-function sensitive for PVS1 auto-tagging
+lof_genes:
+  - BRCA1
+  - BRCA2
+  - TTN
+  - CFTR

configs/panel.example.json

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+{
+  "name": "Hearing loss core",
+  "version": "0.1",
+  "source": "curated",
+  "last_updated": "2024-06-01",
+  "genes": ["GJB2", "SLC26A4", "MITF", "OTOF"],
+  "metadata": {
+    "notes": "Example panel for demo; replace with curated panel and provenance."
+  }
+}

configs/phenotype_to_genes.example.json

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+{
+  "version": "0.1",
+  "source": "example-curated",
+  "phenotype_to_genes": {
+    "HP:0000365": ["GJB2", "SLC26A4", "OTOF"],
+    "HP:0000510": ["MITF", "SOX10"]
+  },
+  "metadata": {
+    "notes": "Placeholder mapping; replace with curated HPO/OMIM/GenCC panels."
+  }
+}

configs/phenotype_to_genes.hpo_seed.json

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+{
+  "version": "2024-11-01",
+  "source": "HPO-curated-seed",
+  "phenotype_to_genes": {
+    "HP:0000365": ["GJB2", "SLC26A4", "OTOF", "TECTA"],
+    "HP:0001250": ["SCN1A", "KCNQ2", "STXBP1"],
+    "HP:0001631": ["MYH7", "TNNT2", "MYBPC3"],
+    "HP:0001156": ["COL1A1", "COL1A2", "PLOD2"]
+  },
+  "metadata": {
+    "notes": "Seed mapping using common phenotype IDs; replace with full HPO-derived panels."
+  }
+}