huggingworld/clinvar-annotations
part of 🧬 Genomic Reasoning Agent LLM-driven agentic system for personal genomic variant interpretation Overview This project builds a multi-step reasoning agent that interprets personal genomic data from 23andMe against biomedical knowledge databases (ClinVar, GWAS Catalog, gnomAD). The agent is trained with GRPO (Group Relative Policy Optimization) using fully verifiable reward signals — no human labelers needed. The core insight mirrors… See the full description on the dataset page: https://huggingface.co/datasets/huggingworld/clinvar-annotations.
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1gene,gene_id,clinical_significance,review_status,variant_type,consequence,protein_change,allele_freq_gnomad,rsid,genotype,chromosome,position,zygosity,conditions,pubmed_ids2MTHFR,4524,Pathogenic/Likely pathogenic,criteria provided multiple submitters,SNV,missense,p.Ala222Val,0.337,rs1801133,GG,1,11856378,homozygous,Homocystinuria,90429093MTHFR,4524,Pathogenic/Likely pathogenic,criteria provided multiple submitters,SNV,missense,p.Ala222Val,0.337,rs1801133,GG,1,11856378,homozygous,Neural tube defects,102153254MTHFR,4524,Pathogenic/Likely pathogenic,criteria provided multiple submitters,SNV,missense,p.Ala222Val,0.337,rs1801133,GG,1,11856378,homozygous,Methylenetetrahydrofolate reductase deficiency,155651115OXTR,5021,Benign,criteria provided single submitter,SNV,intron_variant,,0.378,rs53576,AG,3,8804371,heterozygous,Social behavior,199340466OXTR,5021,Benign,criteria provided single submitter,SNV,intron_variant,,0.378,rs53576,AG,3,8804371,heterozygous,Autism spectrum disorder,207246627PPARG,5468,Benign,criteria provided single submitter,SNV,missense,p.Pro12Ala,0.122,rs1801282,CG,3,12393125,heterozygous,Type 2 diabetes,93332388PPARG,5468,Benign,criteria provided single submitter,SNV,missense,p.Pro12Ala,0.122,rs1801282,CG,3,12393125,heterozygous,Obesity,105810399PPARG,5468,Benign,criteria provided single submitter,SNV,missense,p.Pro12Ala,0.122,rs1801282,CG,3,12393125,heterozygous,Metabolic syndrome,10HFE,3077,Benign,reviewed by expert panel,SNV,missense,p.His63Asp,0.136,rs1799945,CC,6,26091179,homozygous,Hereditary hemochromatosis,911099011HFE,3077,Benign,reviewed by expert panel,SNV,missense,p.His63Asp,0.136,rs1799945,CC,6,26091179,homozygous,Iron overload,12BDNF,627,Benign/Likely benign,criteria provided multiple submitters,SNV,missense,p.Val66Met,0.196,rs6265,CC,11,27679916,homozygous,Major depressive disorder,1117489813BDNF,627,Benign/Likely benign,criteria provided multiple submitters,SNV,missense,p.Val66Met,0.196,rs6265,CC,11,27679916,homozygous,Episodic memory,1467118014BDNF,627,Benign/Likely benign,criteria provided multiple submitters,SNV,missense,p.Val66Met,0.196,rs6265,CC,11,27679916,homozygous,Bipolar disorder susceptibility,15ANKK1,255239,risk factor,criteria provided single submitter,SNV,missense,p.Glu713Lys,0.192,rs1800497,GG,11,113270828,homozygous,Alcohol dependence,130195616ANKK1,255239,risk factor,criteria provided single submitter,SNV,missense,p.Glu713Lys,0.192,rs1800497,GG,11,113270828,homozygous,ADHD,1134923017ANKK1,255239,risk factor,criteria provided single submitter,SNV,missense,p.Glu713Lys,0.192,rs1800497,GG,11,113270828,homozygous,Reward deficiency syndrome,18CYP1A2,1544,drug response,criteria provided single submitter,SNV,intron_variant,,0.681,rs762551,AC,15,75041917,heterozygous,Caffeine metabolism,1002296119CYP1A2,1544,drug response,criteria provided single submitter,SNV,intron_variant,,0.681,rs762551,AC,15,75041917,heterozygous,Drug metabolism — clozapine,1536489020CYP1A2,1544,drug response,criteria provided single submitter,SNV,intron_variant,,0.681,rs762551,AC,15,75041917,heterozygous,PharmGKB — caffeine,21FTO,79068,risk factor,criteria provided multiple submitters,SNV,intron_variant,,0.404,rs9939609,AT,16,53820527,heterozygous,Obesity,1729387722FTO,79068,risk factor,criteria provided multiple submitters,SNV,intron_variant,,0.404,rs9939609,AT,16,53820527,heterozygous,Type 2 diabetes,1746876523FTO,79068,risk factor,criteria provided multiple submitters,SNV,intron_variant,,0.404,rs9939609,AT,16,53820527,heterozygous,Body mass index quantitative trait locus 8,24APOE,348,risk factor,reviewed by expert panel,SNV,missense,p.Cys130Arg,0.154,rs429358,TT,19,45411941,homozygous,Alzheimer disease,844617025APOE,348,risk factor,reviewed by expert panel,SNV,missense,p.Cys130Arg,0.154,rs429358,TT,19,45411941,homozygous,Cardiovascular disease,130323926APOE,348,risk factor,reviewed by expert panel,SNV,missense,p.Cys130Arg,0.154,rs429358,TT,19,45411941,homozygous,Hyperlipoproteinemia type III,27APOE,348,risk factor,reviewed by expert panel,SNV,missense,p.Arg176Cys,0.073,rs7412,CC,19,45412079,homozygous,Alzheimer disease,844617028APOE,348,risk factor,reviewed by expert panel,SNV,missense,p.Arg176Cys,0.073,rs7412,CC,19,45412079,homozygous,Cardiovascular disease,130323929COMT,1312,Benign/Likely benign,criteria provided single submitter,SNV,missense,p.Val158Met,0.502,rs4680,GG,22,19951271,homozygous,Pain sensitivity,963210230COMT,1312,Benign/Likely benign,criteria provided single submitter,SNV,missense,p.Val158Met,0.502,rs4680,GG,22,19951271,homozygous,Schizophrenia susceptibility,1214268831COMT,1312,Benign/Likely benign,criteria provided single submitter,SNV,missense,p.Val158Met,0.502,rs4680,GG,22,19951271,homozygous,Catechol-O-methyltransferase deficiency,32ADORA2A,135,Benign,criteria provided single submitter,SNV,synonymous_variant,,0.463,rs5751876,CT,22,24837301,heterozygous,Caffeine-induced anxiety,1707497733ADORA2A,135,Benign,criteria provided single submitter,SNV,synonymous_variant,,0.463,rs5751876,CT,22,24837301,heterozygous,Sleep sensitivity to caffeine,34