{"id":"W4206004774","doi":"10.1093/nargab/lqab122","title":"A comparison on predicting functional impact of genomic variants","year":2022,"lang":"en","type":"article","venue":"NAR Genomics and Bioinformatics","topic":"Genomics and Rare Diseases","field":"Biochemistry, Genetics and Molecular Biology","cited_by":32,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Calgary","funders":"National Key Research and Development Program of China","keywords":"Single-nucleotide polymorphism; Missense mutation; Genomics; Human genome; Functional genomics; SNP","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000179576,0.0001355526,0.0001682583,0.00007375262,0.0002271228,0.00002239201,0.0001302637,0.00005264839,0.00007446003],"category_scores_gemma":[0.00001536435,0.0001228824,0.0001287893,0.00005223996,0.0000423073,0.000003470783,0.0002543289,0.0001035388,0.000005053489],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00005575887,"about_ca_system_score_gemma":0.000181795,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001549236,"about_ca_topic_score_gemma":0.000001501502,"domain_scores_codex":[0.9991868,0.00002159598,0.0003419013,0.0001429946,0.0001278334,0.0001788821],"domain_scores_gemma":[0.9994465,0.00001284617,0.0002115052,0.0002041701,0.00004033,0.00008465695],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.002965881,0.001431263,0.1676575,0.0002888046,0.001454385,0.00001365346,0.003129795,0.1110661,0.6608862,0.001053118,0.02373825,0.02631509],"study_design_scores_gemma":[0.008230046,0.01484919,0.5519726,0.00004310327,0.0003493431,0.0006890295,0.006393644,0.3424447,0.01220047,0.0004912027,0.0601657,0.002171021],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9975978,0.0003788065,0.0002389278,0.00001660843,0.0001400051,0.000161874,0.0004766779,0.000005890998,0.0009834771],"genre_scores_gemma":[0.9983737,0.000107203,0.0008446917,0.000117238,0.00008784464,0.000009702485,0.0003635516,0.00001503704,0.00008096707],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6486857,"threshold_uncertainty_score":0.5010998,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01467209410687007,"score_gpt":0.2587007337804651,"score_spread":0.244028639673595,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}