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Variant Effect Prediction research benchmarks · SOTA2 Research

Variant Effect Prediction

Benchmarks

Dataset NameSOTA MethodSort

Dataset NameSOTA methodMetricTrendResultsLast Updated

ESM2-150M All-pos MLM+JEPA

0.856Spearman Correlation

32

May 11, 2026

mRNABench Mendelian Variants

58.5AUPR

13

Apr 28, 2026

mRNABench Complex Variants

25.3AUPR

13

Apr 28, 2026

Human SNP (100k+ distance-to-TSS bin)

60.4AUROC

5

May 8, 2026

Human SNP 30–100k distance-to-TSS bin

0.663AUROC

5

May 8, 2026

Human SNP 0–30k distance-to-TSS bin

0.681AUROC

5

May 8, 2026

Songlab ClinVar

0.544AUROC

2

Feb 26, 2026

TraitGym Mendelian

0.544AUROC

2

Feb 26, 2026

TraitGym Complex

49.9AUROC

2

Feb 26, 2026

Popular datasets

Human SNP TraitGym mRNABench ClinVar Variant Effect

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