{"exercise": "FM1_conflicting_records", "handled": true, "summary": "frozen='Uncertain significance' vs live='Likely benign'; cross-citation violations=0; live record cited in final output=False", "live_cited": false, "output": "VERDICT: SUMMARY\n- AlphaMissense score for NM_001875.5(CPS1):c.1226T>C (p.Val409Ala) is 0.196 with classification likely_benign [REC:AM:2:210594569:T>C]\n- ClinVar status for this variant at the 2024-01 freeze was Uncertain significance [REC:CLINVAR:allele1477314]\n- Gene prior for CPS1 from frozen train labels is 0.469, representing the fraction of the gene's frozen train variants labeled pathogenic [REC:GENEPRIOR:CPS1:frozen2024]\n- Calibrated probability of pathogenicity from Build 1's ensemble model is 0.132 [REC:MODEL:ensemble:1477314]", "events": ["retriever: packet has 5 record(s); gate (deterministic) = SUMMARISE", "retriever: local lookup: 4 record(s) in Build 1 universe", "retriever: 1 injected record(s) appended (failure-mode exercise)", "synthesiser: draft written", "critic: round 1 accepted draft"], "usage": {"calls": 2, "prompt_tokens": 1194, "completion_tokens": 289, "total_tokens": 1483}, "check": {"verdict": "SUMMARY", "claims": [{"claim": "AlphaMissense score for NM_001875.5(CPS1):c.1226T>C (p.Val409Ala) is 0.196 with classification likely_benign [REC:AM:2:210594569:T>C]", "cited": ["AM:2:210594569:T>C"], "status": "SUPPORTED", "reason": "citations exist; values match"}, {"claim": "ClinVar status for this variant at the 2024-01 freeze was Uncertain significance [REC:CLINVAR:allele1477314]", "cited": ["CLINVAR:allele1477314"], "status": "SUPPORTED", "reason": "citations exist; values match"}, {"claim": "Gene prior for CPS1 from frozen train labels is 0.469, representing the fraction of the gene's frozen train variants labeled pathogenic [REC:GENEPRIOR:CPS1:frozen2024]", "cited": ["GENEPRIOR:CPS1:frozen2024"], "status": "SUPPORTED", "reason": "citations exist; values match"}, {"claim": "Calibrated probability of pathogenicity from Build 1's ensemble model is 0.132 [REC:MODEL:ensemble:1477314]", "cited": ["MODEL:ensemble:1477314"], "status": "SUPPORTED", "reason": "citations exist; values match"}], "completeness": 0.8, "n_claims": 4}}
{"exercise": "FM2_critic_rejection", "handled": true, "summary": "critic rounds=2, rejections=1, PS3 in final output=False", "output": "VERDICT: SUMMARY\n- The variant NM_005327.7(HADH):c.100G>C (p.Gly34Arg) has an AlphaMissense score of 0.989, classified as likely_pathogenic by AlphaMissense [REC:AM:4:107990032:G>C].\n- ClinVar status at the 2024-01 freeze for this variant shows conflicting interpretations of pathogenicity [REC:CLINVAR:allele631856].\n- The gene prior for HADH is 0.485, based on the fraction of the gene's frozen train variants labelled pathogenic [REC:GENEPRIOR:HADH:frozen2024].\n- The calibrated probability of pathogenicity from the Build 1 ensemble model is 0.962 [REC:MODEL:ensemble:631856].", "events": ["retriever: packet has 4 record(s); gate (deterministic) = SUMMARISE", "retriever: local lookup: 4 record(s) in Build 1 universe", "synthesiser: draft written", "critic: round 1 REJECTED draft \u2014 2 problem(s): bullet 5: No mention of ACMG criterion PS3 or functional studies in any record, AlphaMissense score alone does not fulfill PS3; bullet 0: verdict line violates the gate rule", "synthesiser: revised draft under critic findings", "critic: round 2 accepted draft"], "usage": {"calls": 4, "prompt_tokens": 2246, "completion_tokens": 709, "total_tokens": 2955}, "check": {"verdict": "SUMMARY", "claims": [{"claim": "The variant NM_005327.7(HADH):c.100G>C (p.Gly34Arg) has an AlphaMissense score of 0.989, classified as likely_pathogenic by AlphaMissense [REC:AM:4:107990032:G>C].", "cited": ["AM:4:107990032:G>C"], "status": "SUPPORTED", "reason": "citations exist; values match"}, {"claim": "ClinVar status at the 2024-01 freeze for this variant shows conflicting interpretations of pathogenicity [REC:CLINVAR:allele631856].", "cited": ["CLINVAR:allele631856"], "status": "SUPPORTED", "reason": "citations exist; values match"}, {"claim": "The gene prior for HADH is 0.485, based on the fraction of the gene's frozen train variants labelled pathogenic [REC:GENEPRIOR:HADH:frozen2024].", "cited": ["GENEPRIOR:HADH:frozen2024"], "status": "SUPPORTED", "reason": "citations exist; values match"}, {"claim": "The calibrated probability of pathogenicity from the Build 1 ensemble model is 0.962 [REC:MODEL:ensemble:631856].", "cited": ["MODEL:ensemble:631856"], "status": "SUPPORTED", "reason": "citations exist; values match"}], "completeness": 1.0, "n_claims": 4}}
{"exercise": "FM3_stale_duplicate", "handled": true, "summary": "status claims citing 2024-01 record=1, stale record cited=0", "output": "VERDICT: SUMMARY\n- The AlphaMissense score for the variant NM_005327.7(HADH):c.100G>C (p.Gly34Arg) is 0.989 and it is classified as likely_pathogenic [REC:AM:4:107990032:G>C].\n- ClinVar status at the 2024-01 freeze shows conflicting interpretations of pathogenicity for the variant [REC:CLINVAR:allele631856].\n- The gene prior for HADH is 0.485 based on frozen train labels for variants labelled pathogenic [REC:GENEPRIOR:HADH:frozen2024].\n- The calibrated probability of pathogenicity from Build 1's ensemble model is 0.962 [REC:MODEL:ensemble:631856].", "events": ["retriever: packet has 6 record(s); gate (deterministic) = SUMMARISE", "retriever: local lookup: 4 record(s) in Build 1 universe", "retriever: 2 injected record(s) appended (failure-mode exercise)", "synthesiser: draft written", "critic: round 1 accepted draft"], "usage": {"calls": 2, "prompt_tokens": 1203, "completion_tokens": 312, "total_tokens": 1515}, "check": {"verdict": "SUMMARY", "claims": [{"claim": "The AlphaMissense score for the variant NM_005327.7(HADH):c.100G>C (p.Gly34Arg) is 0.989 and it is classified as likely_pathogenic [REC:AM:4:107990032:G>C].", "cited": ["AM:4:107990032:G>C"], "status": "SUPPORTED", "reason": "citations exist; values match"}, {"claim": "ClinVar status at the 2024-01 freeze shows conflicting interpretations of pathogenicity for the variant [REC:CLINVAR:allele631856].", "cited": ["CLINVAR:allele631856"], "status": "SUPPORTED", "reason": "citations exist; values match"}, {"claim": "The gene prior for HADH is 0.485 based on frozen train labels for variants labelled pathogenic [REC:GENEPRIOR:HADH:frozen2024].", "cited": ["GENEPRIOR:HADH:frozen2024"], "status": "SUPPORTED", "reason": "citations exist; values match"}, {"claim": "The calibrated probability of pathogenicity from Build 1's ensemble model is 0.962 [REC:MODEL:ensemble:631856].", "cited": ["MODEL:ensemble:631856"], "status": "SUPPORTED", "reason": "citations exist; values match"}], "completeness": 0.6666666666666666, "n_claims": 4}}
{"exercise": "FM4_forced_tool_failure", "handled": true, "summary": "completed without exception; verdict=DECLINE; live_errors=['ClinVar live: RuntimeError: simulated tool outage (forced)', 'PubMed live: RuntimeError: simulated tool outage (forced)']", "output": "VERDICT: DECLINE\ninsufficient evidence \u2014 remains VUS", "events": ["retriever: packet has 0 record(s); gate (deterministic) = DECLINE", "retriever: local lookup: 0 record(s) in Build 1 universe", "retriever: live retrieval FAILED (forced outage) \u2014 proceeding with no records", "retriever: live error logged: ClinVar live: RuntimeError: simulated tool outage (forced)", "retriever: live error logged: PubMed live: RuntimeError: simulated tool outage (forced)", "synthesiser: draft written", "critic: round 1 accepted draft"], "usage": {"calls": 2, "prompt_tokens": 606, "completion_tokens": 24, "total_tokens": 630}}