Protocol

Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1)

Zero-shot classification of splice-altering versus other variants in the SpliceVarDB exonic SNVs stratum, AUROC and AUPRC.

16 evaluations · 32 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.

16 recorded evaluations, 32 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

16 evaluations · 32 results. Different protocols are not a single leaderboard.

Protocol: Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1) · Dataset: SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)

Sorted by AUPRC (zero-shot; SpliceVarDB exonic SNVs) (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; SpliceVarDB exonic SNVs)	AUROC (zero-shot; SpliceVarDB exonic SNVs)
SpliceAI (Evo 2 paper variant effect evaluations)Evaluation	0.919 (best in column)	0.934 (best in column)
Pangolin (Evo 2 paper variant effect evaluations)Evaluation	0.822	0.864
CADD (Evo 2 paper variant effect evaluations)Evaluation	0.784	0.799
GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation	0.548	0.675
Evo 2 7B base (Evo 2 paper variant effect evaluations)Evaluation	0.54	0.687
Evo 2 7B (Evo 2 paper variant effect evaluations)Evaluation	0.534	0.681
Evo 2 40B base (Evo 2 paper variant effect evaluations)Evaluation	0.534	0.688
Evo 2 40B (Evo 2 paper variant effect evaluations)Evaluation	0.523	0.684
PhyloP 100 (Evo 2 paper variant effect evaluations)Evaluation	0.498	0.631
PhyloP 470 (Evo 2 paper variant effect evaluations)Evaluation	0.496	0.643
PhyloP 447 (Evo 2 paper variant effect evaluations)Evaluation	0.459	0.61
PhyloP 241 (Evo 2 paper variant effect evaluations)Evaluation	0.452	0.629
AlphaMissense (Evo 2 paper variant effect evaluations)Evaluation	0.449	0.594
RNA-FM (Evo 2 paper variant effect evaluations)Evaluation	0.421	0.56
Evo 1 (Evo 2 paper variant effect evaluations)Evaluation	0.414	0.558
NT (Evo 2 paper variant effect evaluations)Evaluation	0.385	0.49

All 32 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: AlphaMissense (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	0.449 AUPRC (zero-shot; SpliceVarDB exonic SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AlphaMissense on SpliceVarDB exonic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-splicevardb-exonic-snv 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 J497, row 497: Model 'AlphaMissense', Data 'SpliceVarDB', Genomic_Feature 'Exonic', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: AlphaMissense (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	0.594 AUROC (zero-shot; SpliceVarDB exonic SNVs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AlphaMissense on SpliceVarDB exonic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-splicevardb-exonic-snv 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 I497, row 497: Model 'AlphaMissense', Data 'SpliceVarDB', Genomic_Feature 'Exonic', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: CADD (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	0.784 AUPRC (zero-shot; SpliceVarDB exonic SNVs) 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 SpliceVarDB exonic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-splicevardb-exonic-snv 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 J487, row 487: Model 'CADD', Data 'SpliceVarDB', Genomic_Feature 'Exonic', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: CADD (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	0.799 AUROC (zero-shot; SpliceVarDB exonic SNVs) 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 SpliceVarDB exonic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-splicevardb-exonic-snv 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 I487, row 487: Model 'CADD', Data 'SpliceVarDB', Genomic_Feature 'Exonic', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 1 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	0.414 AUPRC (zero-shot; SpliceVarDB exonic SNVs) 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 SpliceVarDB exonic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-splicevardb-exonic-snv 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 J499, row 499: Model 'Evo 1', Data 'SpliceVarDB', Genomic_Feature 'Exonic', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 1 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	0.558 AUROC (zero-shot; SpliceVarDB exonic SNVs) 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 SpliceVarDB exonic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-splicevardb-exonic-snv 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 I499, row 499: Model 'Evo 1', Data 'SpliceVarDB', Genomic_Feature 'Exonic', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	0.534 AUPRC (zero-shot; SpliceVarDB exonic SNVs) 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 SpliceVarDB exonic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-splicevardb-exonic-snv 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 J488, row 488: Model 'Evo 2 40B base', Data 'SpliceVarDB', Genomic_Feature 'Exonic', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	0.688 AUROC (zero-shot; SpliceVarDB exonic SNVs) 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 SpliceVarDB exonic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-splicevardb-exonic-snv 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 I488, row 488: Model 'Evo 2 40B base', Data 'SpliceVarDB', Genomic_Feature 'Exonic', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	0.523 AUPRC (zero-shot; SpliceVarDB exonic SNVs) 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 SpliceVarDB exonic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-splicevardb-exonic-snv 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 J490, row 490: Model 'Evo 2 40B', Data 'SpliceVarDB', Genomic_Feature 'Exonic', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	0.684 AUROC (zero-shot; SpliceVarDB exonic SNVs) 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 SpliceVarDB exonic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-splicevardb-exonic-snv 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 I490, row 490: Model 'Evo 2 40B', Data 'SpliceVarDB', Genomic_Feature 'Exonic', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	0.54 AUPRC (zero-shot; SpliceVarDB exonic SNVs) 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 SpliceVarDB exonic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-splicevardb-exonic-snv 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 J489, row 489: Model 'Evo 2 7B base', Data 'SpliceVarDB', Genomic_Feature 'Exonic', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	0.687 AUROC (zero-shot; SpliceVarDB exonic SNVs) 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 SpliceVarDB exonic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-splicevardb-exonic-snv 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 I489, row 489: Model 'Evo 2 7B base', Data 'SpliceVarDB', Genomic_Feature 'Exonic', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	0.534 AUPRC (zero-shot; SpliceVarDB exonic SNVs) 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 SpliceVarDB exonic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-splicevardb-exonic-snv 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 J491, row 491: Model 'Evo 2 7B', Data 'SpliceVarDB', Genomic_Feature 'Exonic', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	0.681 AUROC (zero-shot; SpliceVarDB exonic SNVs) 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 SpliceVarDB exonic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-splicevardb-exonic-snv 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 I491, row 491: Model 'Evo 2 7B', Data 'SpliceVarDB', Genomic_Feature 'Exonic', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: GPN-MSA (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	0.548 AUPRC (zero-shot; SpliceVarDB exonic SNVs) 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 SpliceVarDB exonic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-splicevardb-exonic-snv 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 J492, row 492: Model 'GPN-MSA', Data 'SpliceVarDB', Genomic_Feature 'Exonic', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: GPN-MSA (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	0.675 AUROC (zero-shot; SpliceVarDB exonic SNVs) 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 SpliceVarDB exonic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-splicevardb-exonic-snv 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 I492, row 492: Model 'GPN-MSA', Data 'SpliceVarDB', Genomic_Feature 'Exonic', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	0.385 AUPRC (zero-shot; SpliceVarDB exonic SNVs) 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 SpliceVarDB exonic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-splicevardb-exonic-snv 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 J500, row 500: Model 'NT', Data 'SpliceVarDB', Genomic_Feature 'Exonic', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	0.49 AUROC (zero-shot; SpliceVarDB exonic SNVs) 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 SpliceVarDB exonic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-splicevardb-exonic-snv 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 I500, row 500: Model 'NT', Data 'SpliceVarDB', Genomic_Feature 'Exonic', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Pangolin (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	0.822 AUPRC (zero-shot; SpliceVarDB exonic SNVs) 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 SpliceVarDB exonic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-splicevardb-exonic-snv 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 J486, row 486: Model 'Pangolin', Data 'SpliceVarDB', Genomic_Feature 'Exonic', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Pangolin (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	0.864 AUROC (zero-shot; SpliceVarDB exonic SNVs) 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 SpliceVarDB exonic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-splicevardb-exonic-snv 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 I486, row 486: Model 'Pangolin', Data 'SpliceVarDB', Genomic_Feature 'Exonic', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	0.498 AUPRC (zero-shot; SpliceVarDB exonic SNVs) 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 SpliceVarDB exonic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-splicevardb-exonic-snv 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 J494, row 494: Model 'phyloP 100', Data 'SpliceVarDB', Genomic_Feature 'Exonic', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	0.631 AUROC (zero-shot; SpliceVarDB exonic SNVs) 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 SpliceVarDB exonic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-splicevardb-exonic-snv 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 I494, row 494: Model 'phyloP 100', Data 'SpliceVarDB', Genomic_Feature 'Exonic', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 241 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	0.452 AUPRC (zero-shot; SpliceVarDB exonic SNVs) 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 SpliceVarDB exonic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-splicevardb-exonic-snv 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 J495, row 495: Model 'phyloP 241', Data 'SpliceVarDB', Genomic_Feature 'Exonic', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: PhyloP 241 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	0.629 AUROC (zero-shot; SpliceVarDB exonic SNVs) 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 SpliceVarDB exonic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-splicevardb-exonic-snv 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 I495, row 495: Model 'phyloP 241', Data 'SpliceVarDB', Genomic_Feature 'Exonic', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 447 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)	0.459 AUPRC (zero-shot; SpliceVarDB exonic SNVs) 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 SpliceVarDB exonic SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-splicevardb-exonic-snv 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 J496, row 496: Model 'phyloP 447', Data 'SpliceVarDB', Genomic_Feature 'Exonic', Variant_Type 'SNV', Sub_category '', column 'AUPRC'

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Author-reported evaluations: 16

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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

3 source records and release history

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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Technical metadata and extraction receipts

Stable ID: gfm-guides-20261014-evo2-brixi2026-protocol-splicevardb-exonic-snv

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 splice-altering versus other variants in the stratum Data 'SpliceVarDB', Genomic_Feature 'Exonic', Variant_Type 'SNV'.
version: As published, Nature 652 (2026), Supplementary Data 1
source locator: Supplementary Data 1 rows with Data 'SpliceVarDB', Genomic_Feature 'Exonic', Variant_Type 'SNV', Sub_category ''; SI A.3.12 and A.3.14 (pages 13 and 14); Fig. 3d
limitations: Positives: 434 splice-altering; negatives: 745 other; total 1179 variants (Supplementary Data 1).; 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: SpliceVarDB experimentally validated splice variants (Brixi et al. 2026)
assessment: AlphaMissense on SpliceVarDB exonic SNVs (Evo 2 paper)
assessment: CADD on SpliceVarDB exonic SNVs (Evo 2 paper)
assessment: Evo 1 on SpliceVarDB exonic SNVs (Evo 2 paper)
assessment: Evo 2 40B base on SpliceVarDB exonic SNVs (Evo 2 paper)
assessment: Evo 2 40B on SpliceVarDB exonic SNVs (Evo 2 paper)
assessment: Evo 2 7B base on SpliceVarDB exonic SNVs (Evo 2 paper)
assessment: Evo 2 7B on SpliceVarDB exonic SNVs (Evo 2 paper)
assessment: GPN-MSA on SpliceVarDB exonic SNVs (Evo 2 paper)
assessment: NT on SpliceVarDB exonic SNVs (Evo 2 paper)
assessment: Pangolin on SpliceVarDB exonic SNVs (Evo 2 paper)
assessment: PhyloP 100 on SpliceVarDB exonic SNVs (Evo 2 paper)
assessment: PhyloP 241 on SpliceVarDB exonic SNVs (Evo 2 paper)
assessment: PhyloP 447 on SpliceVarDB exonic SNVs (Evo 2 paper)
assessment: PhyloP 470 on SpliceVarDB exonic SNVs (Evo 2 paper)
assessment: RNA-FM on SpliceVarDB exonic SNVs (Evo 2 paper)
assessment: SpliceAI on SpliceVarDB exonic SNVs (Evo 2 paper)

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