data/train.csv

id,variant,gene,phenotype,evidence_pack,claim,evidence_binding_map,evidence_gaps,claim_overreach_flags,confidence_calibration,notes,constraints,gold_checklist
VEI-001,"c.1234A>G (p.Lys412Glu)","GENE1","cardiomyopathy","Observed in 1 affected individual. Absent in 500 controls. No segregation. No functional assay. In silico: damaging.","Pathogenic variant causing cardiomyopathy.","Binding: case report and rarity only. In silico supports possible impact.","No segregation; no functional data; no replication; no population frequency context beyond small control set.","Pathogenic label overreach; causality overreach.","Low confidence. Classify as VUS with rationale.","Tests pathogenic overclaim","Under 220 words.","map+gaps+flags+calibration"
VEI-002,"rs999999","GENE2","type 2 diabetes","GWAS p=1e-9. OR 1.05. Non-coding region. Fine-mapping unresolved. No eQTL. No perturbation.","This variant causes diabetes.","Binding: association only with tiny effect size.","No causal mechanism; no functional perturbation; no linkage resolution.","GWAS treated as causal.","Very low confidence for causality. Association only.","GWAS causality error","Under 220 words.","map+gaps+flags+calibration"
VEI-003,"c.250del (frameshift)","GENE3","neurodevelopmental delay","De novo in child. Parentage confirmed. LoF gene known haploinsufficient. Similar LoF reported in 12 cases. Functional: reduced protein.","Pathogenic and likely causal.","Binding: de novo + known LoF mechanism + replication + functional support.","Missing: detailed phenotype match; mosaicism check.","Minor. Evidence mostly adequate.","High confidence. Pathogenic.","Gold-standard case","Under 220 words.","map+gaps+flags+calibration"
VEI-004,"c.88C>T (p.Pro30Leu)","GENE4","epilepsy","In silico: benign in 2 tools, damaging in 1. Seen at 0.5 percent in gnomAD. No case enrichment. No functional.","Likely pathogenic.","Binding: none supportive; population frequency argues against.","No case evidence; no function; frequency too high for rare epilepsy.","Likely pathogenic overreach.","Very low confidence. Likely benign or VUS.","In silico misuse plus frequency ignore","Under 220 words.","map+gaps+flags+calibration"
VEI-005,"chr7:12345 A>G","GENE5","autoimmune phenotype","Cell line assay shows altered expression. No human genetic association. No segregation.","Causal variant for autoimmune disease.","Binding: functional in vitro only.","No human association; no in vivo model; no patient evidence.","Functional assay treated as disease proof.","Low confidence for disease causality. Functional effect only.","Function vs disease leap","Under 220 words.","map+gaps+flags+calibration"
VEI-006,"rs111111","GENE6","lipid levels","GWAS strong. eQTL links to gene expression in liver. CRISPR perturbation in hepatocytes shifts lipid pathway markers.","Causal regulatory variant affecting lipids.","Binding: association + eQTL + perturbation consistent with phenotype.","Missing: replication across ancestries; in vivo validation.","Moderate. Causality plausible but scope limited.","Moderate to high confidence for mechanism. Clinical impact uncertain.","Good causal chain but bounded","Under 220 words.","map+gaps+flags+calibration"
VEI-007,"c.500G>A (p.Arg167His)","GENE7","rare syndrome","Reported in 2 papers but phenotypes differ. Variant also seen in gnomAD 0.1 percent. No functional.","This explains the syndrome.","Binding weak; phenotype mismatch and frequency conflict.","No consistent phenotype; no segregation; no function.","Overclaim; phenotype mismatch ignored.","Low confidence. VUS.","Phenotype drift","Under 220 words.","map+gaps+flags+calibration"
VEI-008,"c.900+1G>T (splice)","GENE8","kidney disease","Splice site loss predicted. RNA shows exon skipping in patient tissue. Segregates in family. Multiple reports.","Pathogenic splice variant causing kidney disease.","Binding: predicted splice + RNA confirmation + segregation + replication.","Missing: penetrance estimate.","Minor. Penetrance uncertainty.","High confidence pathogenic.","Strong evidence binding","Under 220 words.","map+gaps+flags+calibration"
VEI-009,"polygenic_score","MULTI","CAD","PRS AUC 0.62 in one cohort. No external validation. Calibration unknown.","PRS proves genetic cause in this patient.","Binding: modest prediction only.","No individual-level causality; no calibration; no transportability test.","Prediction treated as proof.","Low confidence. Risk stratification only.","PRS misuse","Under 220 words.","map+gaps+flags+calibration"
VEI-010,"c.1201T>C (p.Ile401Thr)","GENE9","cancer predisposition","Missense in tumor suppressor. Observed in tumor only. No germline test. No functional.","Germline pathogenic predisposition variant.","Binding: tumor-only observation.","No germline confirmation; no segregation; no function.","Somatic treated as germline.","Very low confidence. Needs germline testing.","Somatic vs germline boundary","Under 220 words.","map+gaps+flags+calibration"