Contested result

Evo 2 and phyloP: TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) reverses the order

Low severity
Not yet reviewed
Ordering reversal
Different tasks across studies

TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) ranks phyloP above Evo 2 in 2 of 2 comparisons; other studies rank Evo 2 above phyloP in 72 of 84.

An automatic lead, not a finding of error. The results below are shown as published, everywhere on the site, until a reviewer decides otherwise.

Which studies agree

2 papers rank Evo 2 above phyloP in 72 of their 91 comparisons and phyloP higher in 12; 7 are ties. Of those papers, GUANinE v1.1 reveals complementarity… ranks phyloP higher on its own (1 of 1). TraitGym official metrics ranks phyloP above Evo 2 in all 2 of its comparisons.

Rank Evo 2 higher (1): Genome modelling and design across all…
Rank phyloP higher (2): TraitGym official metrics (disagrees), GUANinE v1.1 reveals complementarity…
Mixed (0): none

Each paper sits where at least two thirds of its comparisons point; Mixed means neither model reaches two thirds. The larger, outlined dot is the paper that disagrees.

Evo 2 higherTiephyloP higherNumbers are counts of comparisons; the outlined bar is the paper that disagrees.

Papers compared (3)
Paper	Role	Ranks Evo 2 higher	Ranks phyloP higher	Ties
TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) · Source	Disagrees	0	2	0
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026) and 1 more record · DOI	Agrees	72	11	7
GUANinE v1.1 reveals complementarity of supervised and genomic language models · DOI	Agrees	0	1	0

Comparisons in TraitGym official metrics (2)

Protocol	Dataset	Metric	Evo 2	phyloP	Higher
TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average	TraitGym Complex traits, matched 9 controls	AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all'), unitless	0.139	0.227	phyloP
TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average	TraitGym Mendelian traits, matched 9 controls	AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all'), unitless	0.557	0.696	phyloP

Comparisons in Genome modelling and design across all… (90)

Protocol	Dataset	Metric	Evo 2	phyloP	Higher
Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)	BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	AUPRC (zero-shot; BRCA1 'Both' (coding and noncoding) SNVs), unitless	0.733	0.54	Evo 2
Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)	BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	AUROC (zero-shot; BRCA1 'Both' (coding and noncoding) SNVs), unitless	0.904	0.821	Evo 2
Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1)	BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	AUPRC (zero-shot; BRCA1 coding SNVs), unitless	0.572	0.471	Evo 2
Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1)	BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	AUROC (zero-shot; BRCA1 coding SNVs), unitless	0.843	0.785	Evo 2
Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1)	BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	AUPRC (zero-shot; BRCA1 intronic SNVs), unitless	0.438	0.084	Evo 2
Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1)	BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	AUROC (zero-shot; BRCA1 intronic SNVs), unitless	0.895	0.748	Evo 2
Zero-shot BRCA1 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1)	BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	AUPRC (zero-shot; BRCA1 noncoding SNVs), unitless	0.903	0.796	Evo 2
Zero-shot BRCA1 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1)	BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	AUROC (zero-shot; BRCA1 noncoding SNVs), unitless	0.974	0.913	Evo 2
Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1)	BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	AUPRC (zero-shot; BRCA1 splice region SNVs), unitless	0.919	0.847	Evo 2
Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1)	BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	AUROC (zero-shot; BRCA1 splice region SNVs), unitless	0.959	0.888	Evo 2
Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)	BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	AUPRC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs), unitless	0.57	0.4	Evo 2
Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)	BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	AUROC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs), unitless	0.847	0.76	Evo 2
Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1)	BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	AUPRC (zero-shot; BRCA2 coding SNVs), unitless	0.346	0.325	Evo 2
Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1)	BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	AUROC (zero-shot; BRCA2 coding SNVs), unitless	0.77	0.752	Evo 2
Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1)	BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	AUPRC (zero-shot; BRCA2 noncoding SNVs), unitless	0.786	0.828	phyloP
Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1)	BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	AUROC (zero-shot; BRCA2 noncoding SNVs), unitless	0.91	0.888	Evo 2
Zero-shot ClinVar 'Both' (coding and noncoding) indels classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar 'Both' (coding and noncoding) indels), unitless	0.995	0.968	Evo 2
Zero-shot ClinVar 'Both' (coding and noncoding) indels classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar 'Both' (coding and noncoding) indels), unitless	0.983	0.839	Evo 2
Zero-shot ClinVar 'Both' (coding and noncoding) microsatellite variants classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar 'Both' (coding and noncoding) microsatellite variants), unitless	0.989	0.825	Evo 2
Zero-shot ClinVar 'Both' (coding and noncoding) microsatellite variants classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar 'Both' (coding and noncoding) microsatellite variants), unitless	0.985	0.836	Evo 2
Zero-shot ClinVar 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar 'Both' (coding and noncoding) SNVs), unitless	0.95	0.886	Evo 2
Zero-shot ClinVar 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar 'Both' (coding and noncoding) SNVs), unitless	0.97	0.919	Evo 2
Zero-shot ClinVar coding indels classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar coding indels), unitless	0.957	0.899	Evo 2
Zero-shot ClinVar coding indels classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar coding indels), unitless	0.91	0.777	Evo 2
Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar coding microsatellite variants), unitless	0.824	0.549	Evo 2
Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar coding microsatellite variants), unitless	0.86	0.762	Evo 2
Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar coding non-SNVs, far from splice site), unitless	0.954	0.862	Evo 2
Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar coding non-SNVs, far from splice site), unitless	0.917	0.773	Evo 2
Zero-shot ClinVar coding non-SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar coding non-SNVs, highly conserved), unitless	0.981	0.96	Evo 2
Zero-shot ClinVar coding non-SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar coding non-SNVs, highly conserved), unitless	0.846	0.667	Evo 2
Zero-shot ClinVar coding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar coding non-SNVs, moderately conserved), unitless	0.918	0.811	Evo 2
Zero-shot ClinVar coding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar coding non-SNVs, moderately conserved), unitless	0.813	0.645	Evo 2
Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar coding non-SNVs, not conserved), unitless	0.835	0.61	Evo 2
Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar coding non-SNVs, not conserved), unitless	0.771	0.667	Evo 2
Zero-shot ClinVar coding non-SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar coding non-SNVs, poorly conserved), unitless	0.889	0.602	Evo 2
Zero-shot ClinVar coding non-SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar coding non-SNVs, poorly conserved), unitless	0.82	0.59	Evo 2
Zero-shot ClinVar coding SNVs classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar coding SNVs), unitless	0.889	0.906	phyloP
Zero-shot ClinVar coding SNVs classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar coding SNVs), unitless	0.841	0.857	phyloP
Zero-shot ClinVar coding SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar coding SNVs, far from splice site), unitless	0.885	0.903	phyloP
Zero-shot ClinVar coding SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar coding SNVs, far from splice site), unitless	0.841	0.857	phyloP
Zero-shot ClinVar coding SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar coding SNVs, highly conserved), unitless	0.918	0.922	Tie
Zero-shot ClinVar coding SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar coding SNVs, highly conserved), unitless	0.776	0.783	Tie
Zero-shot ClinVar coding SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar coding SNVs, moderately conserved), unitless	0.686	0.507	Evo 2
Zero-shot ClinVar coding SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar coding SNVs, moderately conserved), unitless	0.833	0.666	Evo 2
Zero-shot ClinVar coding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar coding SNVs, near splice site), unitless	0.931	0.95	phyloP
Zero-shot ClinVar coding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar coding SNVs, near splice site), unitless	0.827	0.865	phyloP
Zero-shot ClinVar coding SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar coding SNVs, not conserved), unitless	0.559	0.175	Evo 2
Zero-shot ClinVar coding SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar coding SNVs, not conserved), unitless	0.881	0.571	Evo 2
Zero-shot ClinVar coding SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar coding SNVs, poorly conserved), unitless	0.635	0.311	Evo 2
Zero-shot ClinVar coding SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar coding SNVs, poorly conserved), unitless	0.874	0.578	Evo 2
Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs), unitless	0.6	0.231	Evo 2
Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs), unitless	0.915	0.779	Evo 2
Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) SNVs classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) SNVs), unitless	0.353	0.341	Evo 2
Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) SNVs classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) SNVs), unitless	0.92	0.897	Evo 2
Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar noncoding indels), unitless	0.917	0.84	Evo 2
Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar noncoding indels), unitless	0.971	0.936	Evo 2
Zero-shot ClinVar noncoding microsatellite variants classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar noncoding microsatellite variants), unitless	1	1	Tie
Zero-shot ClinVar noncoding microsatellite variants classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar noncoding microsatellite variants), unitless	1	1	Tie
Zero-shot ClinVar noncoding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar noncoding non-SNVs, far from splice site), unitless	0.744	0.296	Evo 2
Zero-shot ClinVar noncoding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar noncoding non-SNVs, far from splice site), unitless	0.925	0.826	Evo 2
Zero-shot ClinVar noncoding non-SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar noncoding non-SNVs, highly conserved), unitless	0.974	0.936	Evo 2
Zero-shot ClinVar noncoding non-SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar noncoding non-SNVs, highly conserved), unitless	0.949	0.835	Evo 2
Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar noncoding non-SNVs, intergenic), unitless	0.893	0.917	phyloP
Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar noncoding non-SNVs, intergenic), unitless	0.813	0.875	phyloP
Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved), unitless	0.872	0.335	Evo 2
Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved), unitless	0.96	0.783	Evo 2
Zero-shot ClinVar noncoding non-SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar noncoding non-SNVs, near splice site), unitless	0.963	0.934	Evo 2
Zero-shot ClinVar noncoding non-SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar noncoding non-SNVs, near splice site), unitless	0.968	0.925	Evo 2
Zero-shot ClinVar noncoding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar noncoding non-SNVs, not conserved), unitless	0.362	0.0381	Evo 2
Zero-shot ClinVar noncoding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar noncoding non-SNVs, not conserved), unitless	0.8	0.581	Evo 2
Zero-shot ClinVar noncoding non-SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar noncoding non-SNVs, poorly conserved), unitless	0.508	0.186	Evo 2
Zero-shot ClinVar noncoding non-SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar noncoding non-SNVs, poorly conserved), unitless	0.909	0.802	Evo 2
Zero-shot ClinVar noncoding SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar noncoding SNVs, far from splice site), unitless	0.432	0.106	Evo 2
Zero-shot ClinVar noncoding SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar noncoding SNVs, far from splice site), unitless	0.855	0.713	Evo 2
Zero-shot ClinVar noncoding SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar noncoding SNVs, highly conserved), unitless	0.994	0.991	Tie
Zero-shot ClinVar noncoding SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar noncoding SNVs, highly conserved), unitless	0.965	0.941	Evo 2
Zero-shot ClinVar noncoding SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar noncoding SNVs, intergenic), unitless	0.811	0.896	phyloP
Zero-shot ClinVar noncoding SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar noncoding SNVs, intergenic), unitless	0.877	0.948	phyloP
Zero-shot ClinVar noncoding SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar noncoding SNVs, moderately conserved), unitless	0.801	0.511	Evo 2
Zero-shot ClinVar noncoding SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar noncoding SNVs, moderately conserved), unitless	0.945	0.84	Evo 2
Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar noncoding SNVs, near splice site), unitless	0.997	0.994	Tie
Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar noncoding SNVs, near splice site), unitless	0.988	0.98	Tie
Zero-shot ClinVar noncoding SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar noncoding SNVs, not conserved), unitless	0.4	0.0317	Evo 2
Zero-shot ClinVar noncoding SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar noncoding SNVs, not conserved), unitless	0.851	0.605	Evo 2
Zero-shot ClinVar noncoding SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUPRC (zero-shot; ClinVar noncoding SNVs, poorly conserved), unitless	0.567	0.165	Evo 2
Zero-shot ClinVar noncoding SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1)	ClinVar October 2024 release, filtered (Brixi et al. 2026)	AUROC (zero-shot; ClinVar noncoding SNVs, poorly conserved), unitless	0.897	0.716	Evo 2
Zero-shot SpliceVarDB 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)	SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	AUPRC (zero-shot; SpliceVarDB 'Both' (coding and noncoding) SNVs), unitless	0.873	0.813	Evo 2
Zero-shot SpliceVarDB 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)	SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	AUROC (zero-shot; SpliceVarDB 'Both' (coding and noncoding) SNVs), unitless	0.827	0.772	Evo 2
Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1)	SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	AUPRC (zero-shot; SpliceVarDB exonic SNVs), unitless	0.54	0.498	Evo 2
Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1)	SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	AUROC (zero-shot; SpliceVarDB exonic SNVs), unitless	0.688	0.643	Evo 2

Comparisons in GUANinE v1.1 reveals complementarity… (1)

Protocol	Dataset	Metric	Evo 2	phyloP	Higher
GUANinE v1.1 cadd-snv, Spearman rho x100 (Table 3)	GUANinE cadd-snv test set	Spearman (GUANinE v1.1 test set), unitless	24.5	28.7	phyloP

What disagrees

Other studies: rank Evo 2 above phyloP in 72 of 84 comparisons
This study: ranks phyloP above Evo 2 in 2 of 2 comparisons

Compared: Evo 2, phyloP
Study that disagrees: TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym)
Other studies: Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026), Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026), GUANinE v1.1 reveals complementarity of supervised and genomic language models
Rule: Ordering reversal; different tasks across studies
Model identity: Matched across studies partly through links not yet reviewed

The compared numbers

Each value links to its result record and source. Compare values within one protocol; the rule compares rankings, not raw values across protocols.

In the study that disagrees (4)
Study	Tool	Protocol or benchmark	Metric	Value
TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym)	evo2_40b_absLLR.plus.score (TraitGym)	TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average	AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all')	0.139
TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym)	evo2_40b_LLR.minus.score (TraitGym)	TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average	AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all')	0.557
TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym)	phyloP-241m.plus.score (TraitGym)	TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average	AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all')	0.227
TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym)	phyloP-241m.plus.score (TraitGym)	TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average	AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all')	0.696

In the other studies (171 results)

In the other studies
Study	Tool	Protocol or benchmark	Metric	Value
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B base (Evo 2 paper variant effect evaluations)	Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; BRCA1 intronic SNVs)	0.438
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B base (Evo 2 paper variant effect evaluations)	Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; BRCA1 intronic SNVs)	0.895
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B base (Evo 2 paper variant effect evaluations)	Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; BRCA1 splice region SNVs)	0.919
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B base (Evo 2 paper variant effect evaluations)	Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs)	0.847
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B base (Evo 2 paper variant effect evaluations)	Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; BRCA2 coding SNVs)	0.346
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B base (Evo 2 paper variant effect evaluations)	Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; BRCA2 coding SNVs)	0.77
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar 'Both' (coding and noncoding) indels classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar 'Both' (coding and noncoding) indels)	0.995
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar 'Both' (coding and noncoding) indels classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar 'Both' (coding and noncoding) indels)	0.983
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar 'Both' (coding and noncoding) microsatellite variants classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar 'Both' (coding and noncoding) microsatellite variants)	0.989
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar 'Both' (coding and noncoding) microsatellite variants classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar 'Both' (coding and noncoding) microsatellite variants)	0.985
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding microsatellite variants)	0.86
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding non-SNVs, not conserved)	0.835
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding SNVs, moderately conserved)	0.833
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding SNVs, not conserved)	0.881
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs)	0.915
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding non-SNVs, far from splice site)	0.925
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar noncoding non-SNVs, intergenic)	0.893
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding non-SNVs, intergenic)	0.813
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved)	0.872
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved)	0.96
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding non-SNVs, not conserved)	0.8
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding non-SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar noncoding non-SNVs, poorly conserved)	0.508
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding non-SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding non-SNVs, poorly conserved)	0.909
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar noncoding SNVs, intergenic)	0.811
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding SNVs, intergenic)	0.877
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar noncoding SNVs, moderately conserved)	0.801
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding SNVs, moderately conserved)	0.945
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar noncoding SNVs, poorly conserved)	0.567
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B base (Evo 2 paper variant effect evaluations)	Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; SpliceVarDB exonic SNVs)	0.688
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B (Evo 2 paper variant effect evaluations)	Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; BRCA1 coding SNVs)	0.572
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B (Evo 2 paper variant effect evaluations)	Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; BRCA1 coding SNVs)	0.843
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B (Evo 2 paper variant effect evaluations)	Zero-shot BRCA1 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; BRCA1 noncoding SNVs)	0.903
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B (Evo 2 paper variant effect evaluations)	Zero-shot BRCA1 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; BRCA1 noncoding SNVs)	0.974
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B (Evo 2 paper variant effect evaluations)	Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; BRCA1 splice region SNVs)	0.959
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B (Evo 2 paper variant effect evaluations)	Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; BRCA2 noncoding SNVs)	0.786
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B (Evo 2 paper variant effect evaluations)	Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; BRCA2 noncoding SNVs)	0.91
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar 'Both' (coding and noncoding) SNVs)	0.95
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar 'Both' (coding and noncoding) SNVs)	0.97
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding non-SNVs, moderately conserved)	0.813
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding non-SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding non-SNVs, poorly conserved)	0.889
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding non-SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding non-SNVs, poorly conserved)	0.82
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding SNVs)	0.889
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding SNVs)	0.841
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding SNVs, far from splice site)	0.885
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding SNVs, far from splice site)	0.841
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding SNVs, near splice site)	0.931
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding SNVs, near splice site)	0.827
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs)	0.6
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) SNVs)	0.92
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar noncoding indels)	0.917
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding indels)	0.971
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar noncoding non-SNVs, far from splice site)	0.744
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding non-SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar noncoding non-SNVs, highly conserved)	0.974
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding non-SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding non-SNVs, highly conserved)	0.949
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding non-SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar noncoding non-SNVs, near splice site)	0.963
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding non-SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding non-SNVs, near splice site)	0.968
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar noncoding non-SNVs, not conserved)	0.362
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding SNVs, far from splice site)	0.855
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding SNVs, highly conserved)	0.965
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 40B (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding SNVs, poorly conserved)	0.897
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 7B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding indels classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding indels)	0.957
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 7B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding indels classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding indels)	0.91
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 7B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding non-SNVs, far from splice site)	0.954
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 7B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding non-SNVs, far from splice site)	0.917
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 7B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding non-SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding non-SNVs, highly conserved)	0.846
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 7B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding non-SNVs, moderately conserved)	0.918
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 7B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding SNVs, not conserved)	0.559
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 7B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding SNVs, poorly conserved)	0.635
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 7B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding SNVs, poorly conserved)	0.874
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 7B base (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding SNVs, not conserved)	0.851
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 7B base (Evo 2 paper variant effect evaluations)	Zero-shot SpliceVarDB 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; SpliceVarDB 'Both' (coding and noncoding) SNVs)	0.873
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 7B base (Evo 2 paper variant effect evaluations)	Zero-shot SpliceVarDB 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; SpliceVarDB 'Both' (coding and noncoding) SNVs)	0.827
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 7B base (Evo 2 paper variant effect evaluations)	Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; SpliceVarDB exonic SNVs)	0.54
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 7B (Evo 2 paper variant effect evaluations)	Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; BRCA1 'Both' (coding and noncoding) SNVs)	0.733
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 7B (Evo 2 paper variant effect evaluations)	Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; BRCA1 'Both' (coding and noncoding) SNVs)	0.904
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 7B (Evo 2 paper variant effect evaluations)	Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs)	0.57
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 7B (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding microsatellite variants)	0.824
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 7B (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding non-SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding non-SNVs, highly conserved)	0.981
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 7B (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding non-SNVs, not conserved)	0.771
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 7B (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding SNVs, moderately conserved)	0.686
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 7B (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) SNVs)	0.353
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 7B (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar noncoding SNVs, far from splice site)	0.432
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	Evo 2 7B (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar noncoding SNVs, not conserved)	0.4
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; BRCA1 intronic SNVs)	0.084
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; BRCA2 coding SNVs)	0.325
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; BRCA2 coding SNVs)	0.752
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; BRCA2 noncoding SNVs)	0.828
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; BRCA2 noncoding SNVs)	0.888
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar 'Both' (coding and noncoding) microsatellite variants classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar 'Both' (coding and noncoding) microsatellite variants)	0.825
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar 'Both' (coding and noncoding) SNVs)	0.886
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar 'Both' (coding and noncoding) SNVs)	0.919
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding indels classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding indels)	0.899
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding indels classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding indels)	0.777
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding microsatellite variants)	0.549
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding microsatellite variants classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding microsatellite variants)	0.762
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding non-SNVs, far from splice site)	0.862
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding non-SNVs, far from splice site)	0.773
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding non-SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding non-SNVs, highly conserved)	0.96
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding non-SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding non-SNVs, highly conserved)	0.667
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding non-SNVs, moderately conserved)	0.811
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding non-SNVs, moderately conserved)	0.645
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding non-SNVs, not conserved)	0.667
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding non-SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding non-SNVs, poorly conserved)	0.602
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding SNVs)	0.906
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding SNVs)	0.857
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding SNVs, far from splice site)	0.903
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding SNVs, far from splice site)	0.857
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding SNVs, not conserved)	0.571
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) SNVs)	0.341
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar noncoding non-SNVs, far from splice site)	0.296
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar noncoding non-SNVs, not conserved)	0.038
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding non-SNVs, not conserved)	0.581
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar noncoding SNVs, far from splice site)	0.106
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding SNVs, not conserved)	0.605
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 100 (Evo 2 paper variant effect evaluations)	Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; SpliceVarDB exonic SNVs)	0.498
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 241 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding non-SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding non-SNVs, poorly conserved)	0.59
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 241 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding SNVs, poorly conserved)	0.311
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 241 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) SNVs)	0.897
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 241 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding indels)	0.936
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 241 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding non-SNVs, far from splice site)	0.826
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 241 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar noncoding non-SNVs, intergenic)	0.917
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 241 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding non-SNVs, intergenic)	0.875
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 241 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved)	0.783
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 241 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding non-SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar noncoding non-SNVs, poorly conserved)	0.186
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 241 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding non-SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding non-SNVs, poorly conserved)	0.802
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 241 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar noncoding SNVs, intergenic)	0.896
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 241 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding SNVs, intergenic)	0.948
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 447 (Evo 2 paper variant effect evaluations)	Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; BRCA1 'Both' (coding and noncoding) SNVs)	0.54
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 447 (Evo 2 paper variant effect evaluations)	Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; BRCA1 'Both' (coding and noncoding) SNVs)	0.821
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 447 (Evo 2 paper variant effect evaluations)	Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; BRCA1 coding SNVs)	0.471
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 447 (Evo 2 paper variant effect evaluations)	Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; BRCA1 coding SNVs)	0.785
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 447 (Evo 2 paper variant effect evaluations)	Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; BRCA1 intronic SNVs)	0.748
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 447 (Evo 2 paper variant effect evaluations)	Zero-shot BRCA1 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; BRCA1 noncoding SNVs)	0.796
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 447 (Evo 2 paper variant effect evaluations)	Zero-shot BRCA1 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; BRCA1 noncoding SNVs)	0.913
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 447 (Evo 2 paper variant effect evaluations)	Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; BRCA1 splice region SNVs)	0.847
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 447 (Evo 2 paper variant effect evaluations)	Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; BRCA1 splice region SNVs)	0.888
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 447 (Evo 2 paper variant effect evaluations)	Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs)	0.76
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 447 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding non-SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding non-SNVs, not conserved)	0.61
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 447 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding SNVs, moderately conserved)	0.507
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 447 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding SNVs, moderately conserved)	0.666
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 447 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding SNVs, near splice site)	0.95
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 447 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding SNVs, near splice site)	0.865
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 447 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding SNVs, not conserved)	0.175
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 447 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding SNVs, poorly conserved)	0.578
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 447 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar noncoding non-SNVs, intergenic)	0.917
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 447 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding non-SNVs, intergenic)	0.875
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 447 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding SNVs, far from splice site)	0.713
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 447 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding SNVs, highly conserved)	0.941
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 447 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar noncoding SNVs, moderately conserved)	0.511
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 447 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding SNVs, moderately conserved)	0.84
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 447 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar noncoding SNVs, not conserved)	0.032
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 447 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar noncoding SNVs, poorly conserved)	0.165
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 447 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding SNVs, poorly conserved)	0.716
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 470 (Evo 2 paper variant effect evaluations)	Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs)	0.4
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 470 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar 'Both' (coding and noncoding) indels classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar 'Both' (coding and noncoding) indels)	0.968
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 470 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar 'Both' (coding and noncoding) indels classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar 'Both' (coding and noncoding) indels)	0.839
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 470 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar 'Both' (coding and noncoding) microsatellite variants classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar 'Both' (coding and noncoding) microsatellite variants)	0.836
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 470 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs)	0.231
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 470 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) non-SNVs)	0.779
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 470 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding indels classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar noncoding indels)	0.84
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 470 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding non-SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar noncoding non-SNVs, highly conserved)	0.936
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 470 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding non-SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding non-SNVs, highly conserved)	0.835
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 470 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding non-SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding non-SNVs, intergenic)	0.875
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 470 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding non-SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar noncoding non-SNVs, moderately conserved)	0.335
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 470 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding non-SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar noncoding non-SNVs, near splice site)	0.934
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 470 (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar noncoding non-SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding non-SNVs, near splice site)	0.925
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 470 (Evo 2 paper variant effect evaluations)	Zero-shot SpliceVarDB 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; SpliceVarDB 'Both' (coding and noncoding) SNVs)	0.813
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 470 (Evo 2 paper variant effect evaluations)	Zero-shot SpliceVarDB 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; SpliceVarDB 'Both' (coding and noncoding) SNVs)	0.772
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	PhyloP 470 (Evo 2 paper variant effect evaluations)	Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; SpliceVarDB exonic SNVs)	0.643
GUANinE v1.1 reveals complementarity of supervised and genomic language models	Evo2_1B_base (1% eval (evaluated with 1% of the training set), GUANinE v1.1)	GUANinE v1.1 cadd-snv, Spearman rho x100 (Table 3)	Spearman (GUANinE v1.1 test set)	24.5
GUANinE v1.1 reveals complementarity of supervised and genomic language models	phyloP-30way (zero-shot, GUANinE v1.1)	GUANinE v1.1 cadd-snv, Spearman rho x100 (Table 3)	Spearman (GUANinE v1.1 test set)	28.7

Follow-up

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Finding discrepancy-51caba43dcd013d4 · All contested results · How findings are made and followed up