Contested result

ESM-2 and CADD: Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026) reverses the order

Low severity
Not yet reviewed
Ordering reversal
Different tasks across studies

Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026) ranks CADD above ESM-2 in 14 of 14 comparisons; other studies rank ESM-2 above CADD in 6 of 7.

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

Livesey and Marsh 2025 ranks ESM-2 above CADD in 6 of its 7 comparisons and CADD higher in 1. Genome modelling and design across all… ranks CADD above ESM-2 in all 14 of its comparisons.

Rank ESM-2 higher (1): Livesey and Marsh 2025
Rank CADD higher (1): Genome modelling and design across all… (disagrees)
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.

ESM-2 higherTieCADD higherNumbers are counts of comparisons; the outlined bar is the paper that disagrees.

Papers compared (2)
Paper	Role	Ranks ESM-2 higher	Ranks CADD higher	Ties
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	Disagrees	0	14	0
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) and 1 more record · DOI	Agrees	6	1	0

Comparisons in Genome modelling and design across all… (14)

Protocol	Dataset	Metric	ESM-2	CADD	Higher
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	0.827	0.952	CADD
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	0.677	0.927	CADD
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	0.822	0.949	CADD
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	0.678	0.925	CADD
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	0.895	0.961	CADD
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	0.657	0.883	CADD
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	0.62	0.818	CADD
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	0.706	0.905	CADD
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	0.896	0.977	CADD
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	0.68	0.934	CADD
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	0.493	0.623	CADD
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	0.718	0.88	CADD
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	0.503	0.759	CADD
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	0.696	0.912	CADD

Comparisons in Livesey and Marsh 2025 (7)

Protocol	Dataset	Metric	ESM-2	CADD	Higher
Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense	Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins)	Pairwise win rate (average pairwise win rate against all other VEPs, per-protein AUROC on shared variants, ClinVar P/LP versus gnomAD v4.1 missense, proteins with at least 10 of each), percent	51.4	52.1	CADD
Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets	Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, 36 human DMS sets), percent	72.2	40.3	ESM-2
Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets	Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	Pairwise win rate (average pairwise win rate against the five top-ranked VEPs (column top_5_winrate; the five are not listed in the table), \|Spearman\| with DMS on shared variants, 36 human DMS sets), percent	27.8	2.89	ESM-2
Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, direct assays only	Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, direct DMS assays only), percent	74.2	39	ESM-2
Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, indirect assays only	Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, indirect DMS assays only), percent	70.8	41.2	ESM-2
Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, SNV-accessible substitutions only	Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, SNV-accessible substitutions only), percent	70.5	40.3	ESM-2
Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, SNV-accessible substitutions with gaps filled	Livesey and Marsh 2025 human DMS benchmark set (36 proteins)	Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS, SNV-accessible substitutions, missing predictions filled with the VEP's most benign score), percent	71.1	42	ESM-2

What disagrees

Other studies: rank ESM-2 above CADD in 6 of 7 comparisons
This study: ranks CADD above ESM-2 in 14 of 14 comparisons

Compared: ESM-2, CADD
Study that disagrees: Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026), Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026)
Other studies: Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML), Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8)
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 (28)
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	CADD (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding SNVs)	0.952
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	CADD (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding SNVs)	0.927
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	CADD (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)	0.949
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	CADD (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)	0.925
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	CADD (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)	0.961
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	CADD (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)	0.883
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	CADD (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)	0.818
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	CADD (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)	0.905
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	CADD (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)	0.977
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	CADD (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)	0.934
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	CADD (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)	0.623
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	CADD (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)	0.88
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	CADD (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)	0.759
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	CADD (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)	0.912
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	ESM-2 650M (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUPRC (zero-shot; ClinVar coding SNVs)	0.827
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	ESM-2 650M (Evo 2 paper variant effect evaluations)	Zero-shot ClinVar coding SNVs classification (Evo 2 paper, Supplementary Data 1)	AUROC (zero-shot; ClinVar coding SNVs)	0.677
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	ESM-2 650M (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)	0.822
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	ESM-2 650M (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)	0.678
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	ESM-2 650M (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)	0.895
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	ESM-2 650M (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)	0.657
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	ESM-2 650M (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)	0.62
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	ESM-2 650M (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)	0.706
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	ESM-2 650M (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)	0.896
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	ESM-2 650M (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)	0.68
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	ESM-2 650M (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)	0.493
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	ESM-2 650M (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)	0.718
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	ESM-2 650M (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)	0.503
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026); evo2: Journal full-text XML	ESM-2 650M (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)	0.696

In the other studies (14)
Study	Tool	Protocol or benchmark	Metric	Value
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)	CADD_1.7 (Livesey and Marsh 2025)	Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense	Pairwise win rate (average pairwise win rate against all other VEPs, per-protein AUROC on shared variants, ClinVar P/LP versus gnomAD v4.1 missense, proteins with at least 10 of each)	52.1
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)	ESM2 (Livesey and Marsh 2025)	Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense	Pairwise win rate (average pairwise win rate against all other VEPs, per-protein AUROC on shared variants, ClinVar P/LP versus gnomAD v4.1 missense, proteins with at least 10 of each)	51.4
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)	CADD_1.7 (Livesey and Marsh 2025)	Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets	Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, 36 human DMS sets)	40.3
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)	CADD_1.7 (Livesey and Marsh 2025)	Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets	Pairwise win rate (average pairwise win rate against the five top-ranked VEPs (column top_5_winrate; the five are not listed in the table), \|Spearman\| with DMS on shared variants, 36 human DMS sets)	2.89
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)	ESM2 (Livesey and Marsh 2025)	Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets	Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, 36 human DMS sets)	72.2
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)	ESM2 (Livesey and Marsh 2025)	Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, all 36 DMS sets	Pairwise win rate (average pairwise win rate against the five top-ranked VEPs (column top_5_winrate; the five are not listed in the table), \|Spearman\| with DMS on shared variants, 36 human DMS sets)	27.8
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)	CADD_1.7 (Livesey and Marsh 2025)	Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, direct assays only	Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, direct DMS assays only)	39
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)	ESM2 (Livesey and Marsh 2025)	Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, direct assays only	Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, direct DMS assays only)	74.2
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)	CADD_1.7 (Livesey and Marsh 2025)	Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, indirect assays only	Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, indirect DMS assays only)	41.2
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)	ESM2 (Livesey and Marsh 2025)	Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, indirect assays only	Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, indirect DMS assays only)	70.8
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)	CADD_1.7 (Livesey and Marsh 2025)	Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, SNV-accessible substitutions only	Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, SNV-accessible substitutions only)	40.3
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)	ESM2 (Livesey and Marsh 2025)	Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, SNV-accessible substitutions only	Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS on shared variants, SNV-accessible substitutions only)	70.5
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)	CADD_1.7 (Livesey and Marsh 2025)	Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, SNV-accessible substitutions with gaps filled	Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS, SNV-accessible substitutions, missing predictions filled with the VEP's most benign score)	42
Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)	ESM2 (Livesey and Marsh 2025)	Livesey and Marsh 2025 DMS benchmark: pairwise \|Spearman\| win rate, SNV-accessible substitutions with gaps filled	Pairwise win rate (average pairwise win rate against all other VEPs, \|Spearman\| with DMS, SNV-accessible substitutions, missing predictions filled with the VEP's most benign score)	71.1

Follow-up

Current state: Not yet reviewed.

No one has reviewed this finding yet.

How to help resolve this

If you know why these studies disagree, for example a different population, metric or preprocessing step, or you have a corrected value, tell us through the contribution form. A reviewer checks every submission against its source before anything changes, and the step is added to the follow-up above.

Finding discrepancy-48b2c903acfca584 · All contested results · How findings are made and followed up