Protocol

Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1)

Zero-shot classification of pathogenic/likely pathogenic versus benign/likely benign variants in the ClinVar noncoding SNVs, near splice site stratum, AUROC and AUPRC.

14 evaluations · 28 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.

14 recorded evaluations, 28 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

14 evaluations · 28 results. Different protocols are not a single leaderboard.

Protocol: Zero-shot ClinVar noncoding SNVs, near 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 noncoding SNVs, near 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 noncoding SNVs, near splice site)	AUROC (zero-shot; ClinVar noncoding SNVs, near splice site)
CADD (Evo 2 paper variant effect evaluations)Evaluation	0.998 (best in column)	0.991 (best in column)
Evo 2 40B (Evo 2 paper variant effect evaluations)Evaluation	0.997	0.988
Evo 2 40B base (Evo 2 paper variant effect evaluations)Evaluation	0.997	0.987
PhyloP 470 (Evo 2 paper variant effect evaluations)Evaluation	0.994	0.98
PhyloP 100 (Evo 2 paper variant effect evaluations)Evaluation	0.994	0.978
GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation	0.994	0.977
PhyloP 447 (Evo 2 paper variant effect evaluations)Evaluation	0.994	0.979
PhyloP 241 (Evo 2 paper variant effect evaluations)Evaluation	0.993	0.979
Evo 2 7B (Evo 2 paper variant effect evaluations)Evaluation	0.992	0.972
Evo 2 7B base (Evo 2 paper variant effect evaluations)Evaluation	0.991	0.968
Pangolin (Evo 2 paper variant effect evaluations)Evaluation	0.95	0.827
NT (Evo 2 paper variant effect evaluations)Evaluation	0.841	0.533
Evo 1 (Evo 2 paper variant effect evaluations)Evaluation	0.834	0.551
RNA-FM (Evo 2 paper variant effect evaluations)Evaluation	0.824	0.503

All 28 result rows with coverage, uncertainty and sources

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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: CADD (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.998 AUPRC (zero-shot; ClinVar noncoding SNVs, near 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 CADD on ClinVar noncoding SNVs, near splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-snv-near-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 J195, row 195: Model 'CADD', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Near splice site', column 'AUPRC'
Configuration: CADD (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.991 AUROC (zero-shot; ClinVar noncoding SNVs, near 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 CADD on ClinVar noncoding SNVs, near splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-snv-near-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 I195, row 195: Model 'CADD', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Near splice site', column 'AUROC'
Configuration: Evo 1 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.834 AUPRC (zero-shot; ClinVar noncoding SNVs, near 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 noncoding SNVs, near splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-snv-near-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 J206, row 206: Model 'Evo 1', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Near splice site', column 'AUPRC'
Configuration: Evo 1 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.551 AUROC (zero-shot; ClinVar noncoding SNVs, near 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 noncoding SNVs, near splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-snv-near-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 I206, row 206: Model 'Evo 1', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Near splice site', column 'AUROC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.997 AUPRC (zero-shot; ClinVar noncoding SNVs, near 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 noncoding SNVs, near splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-snv-near-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 J197, row 197: Model 'Evo 2 40B base', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Near splice site', column 'AUPRC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.987 AUROC (zero-shot; ClinVar noncoding SNVs, near 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 noncoding SNVs, near splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-snv-near-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 I197, row 197: Model 'Evo 2 40B base', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Near splice site', column 'AUROC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.997 AUPRC (zero-shot; ClinVar noncoding SNVs, near 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 noncoding SNVs, near splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-snv-near-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 J196, row 196: Model 'Evo 2 40B', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Near splice site', column 'AUPRC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.988 AUROC (zero-shot; ClinVar noncoding SNVs, near 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 noncoding SNVs, near splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-snv-near-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 I196, row 196: Model 'Evo 2 40B', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Near splice site', column 'AUROC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.991 AUPRC (zero-shot; ClinVar noncoding SNVs, near 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 noncoding SNVs, near splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-snv-near-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 J204, row 204: Model 'Evo 2 7B base', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Near splice site', column 'AUPRC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.968 AUROC (zero-shot; ClinVar noncoding SNVs, near 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 noncoding SNVs, near splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-snv-near-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 I204, row 204: Model 'Evo 2 7B base', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Near splice site', column 'AUROC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.992 AUPRC (zero-shot; ClinVar noncoding SNVs, near 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 noncoding SNVs, near splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-snv-near-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 J203, row 203: Model 'Evo 2 7B', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Near splice site', column 'AUPRC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.972 AUROC (zero-shot; ClinVar noncoding SNVs, near 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 noncoding SNVs, near splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-snv-near-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 I203, row 203: Model 'Evo 2 7B', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Near splice site', column 'AUROC'
Configuration: GPN-MSA (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.994 AUPRC (zero-shot; ClinVar noncoding SNVs, near 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 GPN-MSA on ClinVar noncoding SNVs, near splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-snv-near-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 J202, row 202: Model 'GPN-MSA', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Near splice site', column 'AUPRC'
Configuration: GPN-MSA (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.977 AUROC (zero-shot; ClinVar noncoding SNVs, near 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 GPN-MSA on ClinVar noncoding SNVs, near splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-snv-near-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 I202, row 202: Model 'GPN-MSA', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Near splice site', column 'AUROC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.841 AUPRC (zero-shot; ClinVar noncoding SNVs, near 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 noncoding SNVs, near splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-snv-near-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 J207, row 207: Model 'NT', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Near splice site', column 'AUPRC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.533 AUROC (zero-shot; ClinVar noncoding SNVs, near 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 noncoding SNVs, near splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-snv-near-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 I207, row 207: Model 'NT', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Near splice site', column 'AUROC'
Configuration: Pangolin (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.95 AUPRC (zero-shot; ClinVar noncoding SNVs, near 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 Pangolin on ClinVar noncoding SNVs, near splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-snv-near-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 J205, row 205: Model 'Pangolin', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Near splice site', column 'AUPRC'
Configuration: Pangolin (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.827 AUROC (zero-shot; ClinVar noncoding SNVs, near 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 Pangolin on ClinVar noncoding SNVs, near splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-snv-near-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 I205, row 205: Model 'Pangolin', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Near splice site', column 'AUROC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.994 AUPRC (zero-shot; ClinVar noncoding SNVs, near 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 noncoding SNVs, near splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-snv-near-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 J201, row 201: Model 'PhyloP 100', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Near splice site', column 'AUPRC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.978 AUROC (zero-shot; ClinVar noncoding SNVs, near 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 noncoding SNVs, near splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-snv-near-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 I201, row 201: Model 'PhyloP 100', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Near splice site', column 'AUROC'
Configuration: PhyloP 241 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.993 AUPRC (zero-shot; ClinVar noncoding SNVs, near 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 noncoding SNVs, near splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-snv-near-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 J199, row 199: Model 'PhyloP 241', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Near splice site', column 'AUPRC'
Configuration: PhyloP 241 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.979 AUROC (zero-shot; ClinVar noncoding SNVs, near 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 noncoding SNVs, near splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-snv-near-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 I199, row 199: Model 'PhyloP 241', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Near splice site', column 'AUROC'
Configuration: PhyloP 447 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.994 AUPRC (zero-shot; ClinVar noncoding SNVs, near 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 447 on ClinVar noncoding SNVs, near splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-snv-near-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 J200, row 200: Model 'PhyloP 447', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Near splice site', column 'AUPRC'
Configuration: PhyloP 447 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.979 AUROC (zero-shot; ClinVar noncoding SNVs, near 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 447 on ClinVar noncoding SNVs, near splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-snv-near-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 I200, row 200: Model 'PhyloP 447', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Near splice site', column 'AUROC'
Configuration: PhyloP 470 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1) Dataset: ClinVar October 2024 release, filtered (Brixi et al. 2026)	0.994 AUPRC (zero-shot; ClinVar noncoding SNVs, near 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 470 on ClinVar noncoding SNVs, near splice site (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-clinvar-noncoding-snv-near-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 J198, row 198: Model 'PhyloP 470', Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Near 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-noncoding-snv-near-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 'Noncoding', Variant_Type 'SNV', Sub_category 'Near splice site'.
version: As published, Nature 652 (2026), Supplementary Data 1
source locator: Supplementary Data 1 rows with Data 'ClinVar', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category 'Near splice site'; SI A.3.12 and A.3.13 (page 13); Extended Data Fig. 4
limitations: Positives: 7765 pathogenic/likely pathogenic; negatives: 1792 benign/likely benign; total 9557 variants (Supplementary Data 1).; Within 3 bp of the nearest splice donor or 5 bp of the nearest splice acceptor (SI A.3.13).; 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: CADD on ClinVar noncoding SNVs, near splice site (Evo 2 paper)
assessment: Evo 1 on ClinVar noncoding SNVs, near splice site (Evo 2 paper)
assessment: Evo 2 40B base on ClinVar noncoding SNVs, near splice site (Evo 2 paper)
assessment: Evo 2 40B on ClinVar noncoding SNVs, near splice site (Evo 2 paper)
assessment: Evo 2 7B base on ClinVar noncoding SNVs, near splice site (Evo 2 paper)
assessment: Evo 2 7B on ClinVar noncoding SNVs, near splice site (Evo 2 paper)
assessment: GPN-MSA on ClinVar noncoding SNVs, near splice site (Evo 2 paper)
assessment: NT on ClinVar noncoding SNVs, near splice site (Evo 2 paper)
assessment: Pangolin on ClinVar noncoding SNVs, near splice site (Evo 2 paper)
assessment: PhyloP 100 on ClinVar noncoding SNVs, near splice site (Evo 2 paper)
assessment: PhyloP 241 on ClinVar noncoding SNVs, near splice site (Evo 2 paper)
assessment: PhyloP 447 on ClinVar noncoding SNVs, near splice site (Evo 2 paper)
assessment: PhyloP 470 on ClinVar noncoding SNVs, near splice site (Evo 2 paper)
assessment: RNA-FM on ClinVar noncoding SNVs, near splice site (Evo 2 paper)

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