Contested result

GPN-MSA 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
unknown

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

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

3 papers rank GPN-MSA above phyloP in 59 of their 67 comparisons and phyloP higher in 2; 6 are ties. TraitGym official metrics ranks phyloP above GPN-MSA in all 2 of its comparisons.

Rank GPN-MSA higher (2): Genome modelling and design across all…, Genomic heterogeneity inflates…
Rank phyloP higher (1): TraitGym official metrics (disagrees)
Mixed (1): GUANinE v1.1 reveals complementarity…

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.

GPN-MSA higherTiephyloP higherNumbers are counts of comparisons; the outlined bar is the paper that disagrees.

Papers compared (4)
Paper	Role	Ranks GPN-MSA 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	46	2	4
Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) · DOI	Agrees	13	0	1
GUANinE v1.1 reveals complementarity of supervised and genomic language models · DOI	Agrees	0	0	1

Comparisons in TraitGym official metrics (2)

Protocol	Dataset	Metric	GPN-MSA	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	0.224	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	0.654	0.696	phyloP

Comparisons in Genome modelling and design across all… (52)

Protocol	Dataset	Metric	GPN-MSA	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	0.65	0.495	GPN-MSA
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	0.863	0.811	GPN-MSA
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	0.579	0.454	GPN-MSA
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	0.833	0.781	GPN-MSA
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	0.0973	0.084	GPN-MSA
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	0.653	0.637	GPN-MSA
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	0.775	0.709	GPN-MSA
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	0.918	0.898	GPN-MSA
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	0.832	0.784	GPN-MSA
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	0.891	0.873	GPN-MSA
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	0.397	GPN-MSA
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	0.838	0.76	GPN-MSA
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	0.446	0.325	GPN-MSA
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	0.8	0.752	GPN-MSA
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	0.835	0.828	Tie
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	0.905	0.888	GPN-MSA
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	0.944	0.886	GPN-MSA
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	0.959	0.919	GPN-MSA
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	0.932	0.906	GPN-MSA
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	0.896	0.857	GPN-MSA
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	0.929	0.903	GPN-MSA
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	0.896	0.857	GPN-MSA
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	0.941	0.922	GPN-MSA
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	0.824	0.783	GPN-MSA
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	0.748	0.374	GPN-MSA
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	0.866	0.579	GPN-MSA
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	0.962	0.939	GPN-MSA
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	0.896	0.846	GPN-MSA
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	0.762	0.155	GPN-MSA
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	0.916	0.571	GPN-MSA
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	0.708	0.224	GPN-MSA
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	0.882	0.531	GPN-MSA
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	0.36	0.341	GPN-MSA
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	0.915	0.876	GPN-MSA
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	0.132	0.106	GPN-MSA
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	0.723	0.691	GPN-MSA
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	0.951	0.934	GPN-MSA
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	0.87	0.882	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	0.884	0.927	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	0.405	0.164	GPN-MSA
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	0.828	0.697	GPN-MSA
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	0.994	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	0.977	0.978	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	0.0541	0.0159	GPN-MSA
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	0.686	0.605	GPN-MSA
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	0.13	0.026	GPN-MSA
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	0.706	0.547	GPN-MSA
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	0.846	0.806	GPN-MSA
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	0.79	0.76	GPN-MSA
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	0.548	0.498	GPN-MSA
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	0.675	0.631	GPN-MSA

Comparisons in Genomic heterogeneity inflates… (14)

Protocol	Dataset	Metric	GPN-MSA	phyloP	Higher
ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	Lu et al. 2025 ClinVar benchmark: All variants (Figure 1)	AUROC (ClinVar pathogenic vs benign SNVs, All variants), unitless	0.96	0.908	GPN-MSA
ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	Lu et al. 2025 ClinVar benchmark: Intron (Non-splice) (Figure 1)	AUROC (ClinVar pathogenic vs benign SNVs, Intron (Non-splice)), unitless	0.885	0.852	GPN-MSA
ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	Lu et al. 2025 ClinVar benchmark: Missense (Figure 1)	AUROC (ClinVar pathogenic vs benign SNVs, Missense), unitless	0.906	0.856	GPN-MSA
ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	Lu et al. 2025 ClinVar benchmark: Missense & Intron (Non-splice) (Figure 1)	AUROC (ClinVar pathogenic vs benign SNVs, Missense & Intron (Non-splice)), unitless	0.896	0.868	GPN-MSA
ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	Lu et al. 2025 ClinVar benchmark: Missense & 3'UTR (Figure 1)	AUROC (ClinVar pathogenic vs benign SNVs, Missense & 3'UTR), unitless	0.887	0.853	GPN-MSA
ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	Lu et al. 2025 ClinVar benchmark: Noncoding (Figure 1)	AUROC (ClinVar pathogenic vs benign SNVs, Noncoding), unitless	0.981	0.976	Tie
ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	Lu et al. 2025 ClinVar benchmark: RNA gene (Figure 1)	AUROC (ClinVar pathogenic vs benign SNVs, RNA gene), unitless	0.938	0.882	GPN-MSA
ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	Lu et al. 2025 ClinVar benchmark: Splice (Figure 1)	AUROC (ClinVar pathogenic vs benign SNVs, Splice), unitless	0.775	0.727	GPN-MSA
ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	Lu et al. 2025 ClinVar benchmark: Start loss (Figure 1)	AUROC (ClinVar pathogenic vs benign SNVs, Start loss), unitless	0.769	0.675	GPN-MSA
ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	Lu et al. 2025 ClinVar benchmark: Stop gain (Figure 1)	AUROC (ClinVar pathogenic vs benign SNVs, Stop gain), unitless	0.783	0.704	GPN-MSA
ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	Lu et al. 2025 ClinVar benchmark: Stop loss (Figure 1)	AUROC (ClinVar pathogenic vs benign SNVs, Stop loss), unitless	0.888	0.796	GPN-MSA
ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	Lu et al. 2025 ClinVar benchmark: Synonymous (Figure 1)	AUROC (ClinVar pathogenic vs benign SNVs, Synonymous), unitless	0.882	0.855	GPN-MSA
ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	Lu et al. 2025 ClinVar benchmark: 3' UTR (Figure 1)	AUROC (ClinVar pathogenic vs benign SNVs, 3' UTR), unitless	0.908	0.862	GPN-MSA
ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	Lu et al. 2025 ClinVar benchmark: 5' UTR (Figure 1)	AUROC (ClinVar pathogenic vs benign SNVs, 5' UTR), unitless	0.728	0.696	GPN-MSA

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

Protocol	Dataset	Metric	GPN-MSA	phyloP	Higher
GUANinE v1.1 clinvar-snv, Spearman rho x100 (Table 4)	GUANinE clinvar-snv test set	Spearman (GUANinE v1.1 test set), unitless	80.7	81.5	Tie

What disagrees

Other studies: rank GPN-MSA above phyloP in 59 of 61 comparisons
This study: ranks phyloP above GPN-MSA in 2 of 2 comparisons

Compared: GPN-MSA, 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), Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2)
Rule: Ordering reversal; unknown
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)	GPN-MSA_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')	0.224
TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym)	GPN-MSA_absLLR.plus.score (TraitGym)	TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average	AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all')	0.654
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 (122 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	GPN-MSA (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)	0.65
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	GPN-MSA (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)	0.863
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	GPN-MSA (Evo 2 paper variant effect evaluations)	Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; BRCA1 coding SNVs)	0.579
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	GPN-MSA (Evo 2 paper variant effect evaluations)	Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; BRCA1 coding SNVs)	0.833
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	GPN-MSA (Evo 2 paper variant effect evaluations)	Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; BRCA1 intronic SNVs)	0.097
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	GPN-MSA (Evo 2 paper variant effect evaluations)	Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; BRCA1 intronic SNVs)	0.653
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	GPN-MSA (Evo 2 paper variant effect evaluations)	Zero-shot BRCA1 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; BRCA1 noncoding SNVs)	0.775
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	GPN-MSA (Evo 2 paper variant effect evaluations)	Zero-shot BRCA1 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; BRCA1 noncoding SNVs)	0.918
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	GPN-MSA (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)	0.832
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	GPN-MSA (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)	0.891
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	GPN-MSA (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	GPN-MSA (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)	0.838
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	GPN-MSA (Evo 2 paper variant effect evaluations)	Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; BRCA2 coding SNVs)	0.446
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	GPN-MSA (Evo 2 paper variant effect evaluations)	Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; BRCA2 coding SNVs)	0.8
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	GPN-MSA (Evo 2 paper variant effect evaluations)	Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; BRCA2 noncoding SNVs)	0.905
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	GPN-MSA (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)	0.944
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	GPN-MSA (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)	0.959
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	GPN-MSA (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding SNVs)	0.932
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	GPN-MSA (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding SNVs)	0.896
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	GPN-MSA (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)	0.929
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	GPN-MSA (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)	0.896
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	GPN-MSA (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding 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	GPN-MSA (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding SNVs, highly conserved)	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	GPN-MSA (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)	0.748
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	GPN-MSA (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)	0.866
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	GPN-MSA (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)	0.962
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	GPN-MSA (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)	0.896
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	GPN-MSA (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)	0.762
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	GPN-MSA (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)	0.916
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	GPN-MSA (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)	0.708
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	GPN-MSA (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)	0.882
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	GPN-MSA (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)	0.36
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	GPN-MSA (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)	0.915
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	GPN-MSA (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)	0.132
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	GPN-MSA (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)	0.723
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	GPN-MSA (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)	0.951
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	GPN-MSA (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)	0.87
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	GPN-MSA (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)	0.884
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	GPN-MSA (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)	0.405
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	GPN-MSA (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)	0.828
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	GPN-MSA (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)	0.054
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	GPN-MSA (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)	0.686
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	GPN-MSA (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)	0.13
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	GPN-MSA (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)	0.706
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	GPN-MSA (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)	0.846
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	GPN-MSA (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)	0.79
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	GPN-MSA (Evo 2 paper variant effect evaluations)	Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; SpliceVarDB exonic SNVs)	0.548
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	GPN-MSA (Evo 2 paper variant effect evaluations)	Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; SpliceVarDB exonic SNVs)	0.675
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 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; BRCA1 'Both' (coding and noncoding) SNVs)	0.495
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 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; BRCA1 'Both' (coding and noncoding) SNVs)	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 BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; BRCA1 coding SNVs)	0.454
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 coding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; BRCA1 coding SNVs)	0.781
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 BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; BRCA1 intronic SNVs)	0.637
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 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; BRCA1 noncoding SNVs)	0.709
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 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; BRCA1 noncoding SNVs)	0.898
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 splice region SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; BRCA1 splice region SNVs)	0.784
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 splice region SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; BRCA1 splice region 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	PhyloP 100 (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)	0.397
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 '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 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)	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) 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 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, highly conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding SNVs, highly conserved)	0.922
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, highly conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding SNVs, highly 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 100 (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)	0.374
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, moderately conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding SNVs, moderately conserved)	0.579
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, near splice site classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding SNVs, near splice site)	0.939
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, near splice site classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding SNVs, near splice site)	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	PhyloP 100 (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)	0.155
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 coding SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding SNVs, poorly conserved)	0.224
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, poorly conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding SNVs, poorly conserved)	0.531
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 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)	0.876
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, far from splice site classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding SNVs, far from splice site)	0.691
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, highly conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding SNVs, highly conserved)	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 100 (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)	0.882
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, intergenic classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding SNVs, intergenic)	0.927
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, moderately conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar noncoding SNVs, moderately conserved)	0.164
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, moderately conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding SNVs, moderately conserved)	0.697
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)	AUPRC (zero-shot; ClinVar noncoding SNVs, not conserved)	0.016
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 ClinVar noncoding SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar noncoding SNVs, poorly conserved)	0.026
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, poorly conserved classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar noncoding SNVs, poorly conserved)	0.547
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 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; SpliceVarDB 'Both' (coding and noncoding) SNVs)	0.806
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 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; SpliceVarDB '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 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 100 (Evo 2 paper variant effect evaluations)	Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; SpliceVarDB exonic SNVs)	0.631
Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2)	GPN-MSA precomputed hg38 scores (Lu et al. 2025)	ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	AUROC (ClinVar pathogenic vs benign SNVs, All variants)	0.96
Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2)	PhyloP 100-way vertebrate (Lu et al. 2025)	ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	AUROC (ClinVar pathogenic vs benign SNVs, All variants)	0.908
Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2)	GPN-MSA precomputed hg38 scores (Lu et al. 2025)	ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	AUROC (ClinVar pathogenic vs benign SNVs, Intron (Non-splice))	0.885
Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2)	PhyloP 100-way vertebrate (Lu et al. 2025)	ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	AUROC (ClinVar pathogenic vs benign SNVs, Intron (Non-splice))	0.852
Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2)	GPN-MSA precomputed hg38 scores (Lu et al. 2025)	ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	AUROC (ClinVar pathogenic vs benign SNVs, Missense & Intron (Non-splice))	0.896
Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2)	PhyloP 100-way vertebrate (Lu et al. 2025)	ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	AUROC (ClinVar pathogenic vs benign SNVs, Missense & Intron (Non-splice))	0.868
Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2)	GPN-MSA precomputed hg38 scores (Lu et al. 2025)	ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	AUROC (ClinVar pathogenic vs benign SNVs, Missense & 3'UTR)	0.887
Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2)	PhyloP 100-way vertebrate (Lu et al. 2025)	ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	AUROC (ClinVar pathogenic vs benign SNVs, Missense & 3'UTR)	0.853
Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2)	GPN-MSA precomputed hg38 scores (Lu et al. 2025)	ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	AUROC (ClinVar pathogenic vs benign SNVs, Missense)	0.906
Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2)	PhyloP 100-way vertebrate (Lu et al. 2025)	ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	AUROC (ClinVar pathogenic vs benign SNVs, Missense)	0.856
Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2)	GPN-MSA precomputed hg38 scores (Lu et al. 2025)	ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	AUROC (ClinVar pathogenic vs benign SNVs, RNA gene)	0.938
Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2)	PhyloP 100-way vertebrate (Lu et al. 2025)	ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	AUROC (ClinVar pathogenic vs benign SNVs, RNA gene)	0.882
Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2)	GPN-MSA precomputed hg38 scores (Lu et al. 2025)	ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	AUROC (ClinVar pathogenic vs benign SNVs, Splice)	0.775
Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2)	PhyloP 100-way vertebrate (Lu et al. 2025)	ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	AUROC (ClinVar pathogenic vs benign SNVs, Splice)	0.727
Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2)	GPN-MSA precomputed hg38 scores (Lu et al. 2025)	ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	AUROC (ClinVar pathogenic vs benign SNVs, Start loss)	0.769
Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2)	PhyloP 100-way vertebrate (Lu et al. 2025)	ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	AUROC (ClinVar pathogenic vs benign SNVs, Start loss)	0.675
Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2)	GPN-MSA precomputed hg38 scores (Lu et al. 2025)	ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	AUROC (ClinVar pathogenic vs benign SNVs, Stop gain)	0.783
Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2)	PhyloP 100-way vertebrate (Lu et al. 2025)	ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	AUROC (ClinVar pathogenic vs benign SNVs, Stop gain)	0.704
Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2)	GPN-MSA precomputed hg38 scores (Lu et al. 2025)	ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	AUROC (ClinVar pathogenic vs benign SNVs, Stop loss)	0.888
Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2)	PhyloP 100-way vertebrate (Lu et al. 2025)	ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	AUROC (ClinVar pathogenic vs benign SNVs, Stop loss)	0.796
Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2)	GPN-MSA precomputed hg38 scores (Lu et al. 2025)	ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	AUROC (ClinVar pathogenic vs benign SNVs, Synonymous)	0.882
Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2)	PhyloP 100-way vertebrate (Lu et al. 2025)	ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	AUROC (ClinVar pathogenic vs benign SNVs, Synonymous)	0.855
Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2)	GPN-MSA precomputed hg38 scores (Lu et al. 2025)	ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	AUROC (ClinVar pathogenic vs benign SNVs, 3' UTR)	0.908
Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2)	PhyloP 100-way vertebrate (Lu et al. 2025)	ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	AUROC (ClinVar pathogenic vs benign SNVs, 3' UTR)	0.862
Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2)	GPN-MSA precomputed hg38 scores (Lu et al. 2025)	ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	AUROC (ClinVar pathogenic vs benign SNVs, 5' UTR)	0.728
Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2)	PhyloP 100-way vertebrate (Lu et al. 2025)	ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)	AUROC (ClinVar pathogenic vs benign SNVs, 5' UTR)	0.696

Follow-up

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Finding discrepancy-8028d0bd151d6c00 · All contested results · How findings are made and followed up