Protocol

Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1)

Zero-shot classification of pathogenic/likely pathogenic versus benign/likely benign variants in the ClinVar coding non-SNVs, far from splice site stratum, AUROC and AUPRC.

15 evaluations · 30 results

Overview

An explanatory profile has not yet been reviewed for this record.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

15 recorded evaluations, 30 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

View coverage and remaining gaps across all benchmarks

Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

15 evaluations · 30 results. Different protocols are not a single leaderboard.

Protocol: Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) · Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)

Sorted by AUPRC (zero-shot; ClinVar coding non-SNVs, far from splice site) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	AUPRC (zero-shot; ClinVar coding non-SNVs, far from splice site)	AUROC (zero-shot; ClinVar coding non-SNVs, far from splice site)
Evo 2 7B base (Evo 2 paper variant effect evaluations)Evaluation	0.954 (best in column)	0.917 (best in column)
Evo 2 7B (Evo 2 paper variant effect evaluations)Evaluation	0.953	0.914
Evo 2 40B base (Evo 2 paper variant effect evaluations)Evaluation	0.948	0.912
Evo 2 40B (Evo 2 paper variant effect evaluations)Evaluation	0.948	0.911
ESM-1b (Evo 2 paper variant effect evaluations)Evaluation	0.92	0.808
DeCodon 200M (Evo 2 paper variant effect evaluations)Evaluation	0.896	0.777
PhyloP 100 (Evo 2 paper variant effect evaluations)Evaluation	0.862	0.773
PhyloP 470 (Evo 2 paper variant effect evaluations)Evaluation	0.82	0.738
PhyloP 447 (Evo 2 paper variant effect evaluations)Evaluation	0.808	0.716
PhyloP 241 (Evo 2 paper variant effect evaluations)Evaluation	0.801	0.707
Evo 1 (Evo 2 paper variant effect evaluations)Evaluation	0.778	0.687
CodonBERT 87M (Evo 2 paper variant effect evaluations)Evaluation	0.748	0.544
ESM-2 650M (Evo 2 paper variant effect evaluations)Evaluation	0.741	0.531
EnCodon 620M (Evo 2 paper variant effect evaluations)Evaluation	0.73	0.519
NT (Evo 2 paper variant effect evaluations)Evaluation	0.671	0.507

All 30 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: CodonBERT 87M (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.748 AUPRC (zero-shot; ClinVar coding non-SNVs, far from splice site) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CodonBERT 87M on ClinVar coding non-SNVs, far from splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-far-from-splice-site Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J163, row 163: Model 'CodonBERT 87M', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Far from splice site', column 'AUPRC'
Configuration: CodonBERT 87M (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.544 AUROC (zero-shot; ClinVar coding non-SNVs, far from splice site) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CodonBERT 87M on ClinVar coding non-SNVs, far from splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-far-from-splice-site Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I163, row 163: Model 'CodonBERT 87M', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Far from splice site', column 'AUROC'
Configuration: DeCodon 200M (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.896 AUPRC (zero-shot; ClinVar coding non-SNVs, far from splice site) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DeCodon 200M on ClinVar coding non-SNVs, far from splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-far-from-splice-site Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J157, row 157: Model 'DeCodon 200M', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Far from splice site', column 'AUPRC'
Configuration: DeCodon 200M (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.777 AUROC (zero-shot; ClinVar coding non-SNVs, far from splice site) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DeCodon 200M on ClinVar coding non-SNVs, far from splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-far-from-splice-site Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I157, row 157: Model 'DeCodon 200M', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Far from splice site', column 'AUROC'
Configuration: EnCodon 620M (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.73 AUPRC (zero-shot; ClinVar coding non-SNVs, far from splice site) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EnCodon 620M on ClinVar coding non-SNVs, far from splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-far-from-splice-site Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J165, row 165: Model 'EnCodon 620M', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Far from splice site', column 'AUPRC'
Configuration: EnCodon 620M (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.519 AUROC (zero-shot; ClinVar coding non-SNVs, far from splice site) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EnCodon 620M on ClinVar coding non-SNVs, far from splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-far-from-splice-site Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I165, row 165: Model 'EnCodon 620M', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Far from splice site', column 'AUROC'
Configuration: ESM-1b (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.92 AUPRC (zero-shot; ClinVar coding non-SNVs, far from splice site) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM-1b on ClinVar coding non-SNVs, far from splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-far-from-splice-site Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J156, row 156: Model 'ESM-1b', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Far from splice site', column 'AUPRC'
Configuration: ESM-1b (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.808 AUROC (zero-shot; ClinVar coding non-SNVs, far from splice site) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM-1b on ClinVar coding non-SNVs, far from splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-far-from-splice-site Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I156, row 156: Model 'ESM-1b', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Far from splice site', column 'AUROC'
Configuration: ESM-2 650M (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.741 AUPRC (zero-shot; ClinVar coding non-SNVs, far from splice site) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM-2 650M on ClinVar coding non-SNVs, far from splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-far-from-splice-site Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J164, row 164: Model 'ESM-2 650M', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Far from splice site', column 'AUPRC'
Configuration: ESM-2 650M (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.531 AUROC (zero-shot; ClinVar coding non-SNVs, far from splice site) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM-2 650M on ClinVar coding non-SNVs, far from splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-far-from-splice-site Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I164, row 164: Model 'ESM-2 650M', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Far from splice site', column 'AUROC'
Configuration: Evo 1 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.778 AUPRC (zero-shot; ClinVar coding non-SNVs, far from splice site) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Evo 1 on ClinVar coding non-SNVs, far from splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-far-from-splice-site Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J162, row 162: Model 'Evo 1', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Far from splice site', column 'AUPRC'
Configuration: Evo 1 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.687 AUROC (zero-shot; ClinVar coding non-SNVs, far from splice site) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Evo 1 on ClinVar coding non-SNVs, far from splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-far-from-splice-site Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I162, row 162: Model 'Evo 1', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Far from splice site', column 'AUROC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.948 AUPRC (zero-shot; ClinVar coding non-SNVs, far from splice site) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Evo 2 40B base on ClinVar coding non-SNVs, far from splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-far-from-splice-site Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J154, row 154: Model 'Evo 2 40B base', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Far from splice site', column 'AUPRC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.912 AUROC (zero-shot; ClinVar coding non-SNVs, far from splice site) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Evo 2 40B base on ClinVar coding non-SNVs, far from splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-far-from-splice-site Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I154, row 154: Model 'Evo 2 40B base', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Far from splice site', column 'AUROC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.948 AUPRC (zero-shot; ClinVar coding non-SNVs, far from splice site) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Evo 2 40B on ClinVar coding non-SNVs, far from splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-far-from-splice-site Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J155, row 155: Model 'Evo 2 40B', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Far from splice site', column 'AUPRC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.911 AUROC (zero-shot; ClinVar coding non-SNVs, far from splice site) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Evo 2 40B on ClinVar coding non-SNVs, far from splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-far-from-splice-site Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I155, row 155: Model 'Evo 2 40B', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Far from splice site', column 'AUROC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.954 AUPRC (zero-shot; ClinVar coding non-SNVs, far from splice site) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Evo 2 7B base on ClinVar coding non-SNVs, far from splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-far-from-splice-site Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J152, row 152: Model 'Evo 2 7B base', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Far from splice site', column 'AUPRC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.917 AUROC (zero-shot; ClinVar coding non-SNVs, far from splice site) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Evo 2 7B base on ClinVar coding non-SNVs, far from splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-far-from-splice-site Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I152, row 152: Model 'Evo 2 7B base', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Far from splice site', column 'AUROC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.953 AUPRC (zero-shot; ClinVar coding non-SNVs, far from splice site) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Evo 2 7B on ClinVar coding non-SNVs, far from splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-far-from-splice-site Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J153, row 153: Model 'Evo 2 7B', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Far from splice site', column 'AUPRC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.914 AUROC (zero-shot; ClinVar coding non-SNVs, far from splice site) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Evo 2 7B on ClinVar coding non-SNVs, far from splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-far-from-splice-site Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I153, row 153: Model 'Evo 2 7B', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Far from splice site', column 'AUROC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.671 AUPRC (zero-shot; ClinVar coding non-SNVs, far from splice site) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NT on ClinVar coding non-SNVs, far from splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-far-from-splice-site Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J166, row 166: Model 'NT', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Far from splice site', column 'AUPRC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.507 AUROC (zero-shot; ClinVar coding non-SNVs, far from splice site) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NT on ClinVar coding non-SNVs, far from splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-far-from-splice-site Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I166, row 166: Model 'NT', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Far from splice site', column 'AUROC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.862 AUPRC (zero-shot; ClinVar coding non-SNVs, far from splice site) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source PhyloP 100 on ClinVar coding non-SNVs, far from splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-far-from-splice-site Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J158, row 158: Model 'PhyloP 100', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Far from splice site', column 'AUPRC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.773 AUROC (zero-shot; ClinVar coding non-SNVs, far from splice site) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source PhyloP 100 on ClinVar coding non-SNVs, far from splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-far-from-splice-site Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell I158, row 158: Model 'PhyloP 100', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Far from splice site', column 'AUROC'
Configuration: PhyloP 241 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar coding non-SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.801 AUPRC (zero-shot; ClinVar coding non-SNVs, far from splice site) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source PhyloP 241 on ClinVar coding non-SNVs, far from splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-far-from-splice-site Aggregation: Not reported Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026); Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Supplementary Data 1 (sheet 'Sheet1') cell J161, row 161: Model 'PhyloP 241', Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Far from splice site', column 'AUPRC'

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evo2: Journal full-text XML · Original source · Retrieved page snapshot; no immutable publisher revision supplied
Genome modelling and design across all domains of life with Evo 2: Supplementary Information (Nature 2026) · Original source · Nature 652 (2026), published 2026-03-04; Supplementary Information file 41586_2026_10176_MOESM1_ESM.pdf (73 pages)
Genome modelling and design across all domains of life with Evo 2: Supplementary Data 1, human variant effect prediction results (Nature 2026) · Original source · Nature 652 (2026), published 2026-03-04; Supplementary Data 1 file 41586_2026_10176_MOESM3_ESM.xlsx

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Stable ID: gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-coding-non-snv-far-from-splice-site

areas: dna-genomes
contexts: research
protocol: Score each variant zero-shot (for Evo 2, the log-likelihood of the variant sequence minus that of the reference over an 8,192-bp genomic window around the variant) and compute AUROC and AUPRC for pathogenic/likely pathogenic versus benign/likely benign variants in the stratum Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Far from splice site'.
version: As published, Nature 652 (2026), Supplementary Data 1
source locator: Supplementary Data 1 rows with Data 'ClinVar', Genomic_Feature 'Coding', Variant_Type 'non-SNV', Sub_category 'Far from splice site'; SI A.3.12 and A.3.13 (page 13); Extended Data Fig. 4
limitations: Positives: 788 pathogenic/likely pathogenic; negatives: 382 benign/likely benign; total 1170 variants (Supplementary Data 1).; Label 'Far from splice site'; SI A.3.13 defines only 'Near to splice site'.; No split: every model scores the same variants zero-shot (SI A.3.12: 'For each benchmark, we score the same variants with all models').; Supervised comparators (AlphaMissense, CADD, SpliceAI, Pangolin) may have been trained on overlapping variants; training overlap is not reported.; No uncertainty is reported.

Related records

part of: Evo 2 paper zero-shot human variant effect evaluations (Brixi et al. 2026)
uses data: ClinVar October 2024 release, filtered (Brixi et al. 2026)
assessment: CodonBERT 87M on ClinVar coding non-SNVs, far from splice site (Evo 2 paper)
assessment: DeCodon 200M on ClinVar coding non-SNVs, far from splice site (Evo 2 paper)
assessment: EnCodon 620M on ClinVar coding non-SNVs, far from splice site (Evo 2 paper)
assessment: ESM-1b on ClinVar coding non-SNVs, far from splice site (Evo 2 paper)
assessment: ESM-2 650M on ClinVar coding non-SNVs, far from splice site (Evo 2 paper)
assessment: Evo 1 on ClinVar coding non-SNVs, far from splice site (Evo 2 paper)
assessment: Evo 2 40B base on ClinVar coding non-SNVs, far from splice site (Evo 2 paper)
assessment: Evo 2 40B on ClinVar coding non-SNVs, far from splice site (Evo 2 paper)
assessment: Evo 2 7B base on ClinVar coding non-SNVs, far from splice site (Evo 2 paper)
assessment: Evo 2 7B on ClinVar coding non-SNVs, far from splice site (Evo 2 paper)
assessment: NT on ClinVar coding non-SNVs, far from splice site (Evo 2 paper)
assessment: PhyloP 100 on ClinVar coding non-SNVs, far from splice site (Evo 2 paper)
assessment: PhyloP 241 on ClinVar coding non-SNVs, far from splice site (Evo 2 paper)
assessment: PhyloP 447 on ClinVar coding non-SNVs, far from splice site (Evo 2 paper)
assessment: PhyloP 470 on ClinVar coding non-SNVs, far from splice site (Evo 2 paper)

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