Protocol

Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1)

Zero-shot classification of loss-of-function (P classes) versus functional (B classes) variants in the BRCA2 noncoding SNVs stratum, AUROC and AUPRC.

15 evaluations · 30 results

Overview

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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.

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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 BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1) · Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)

Sorted by AUPRC (zero-shot; BRCA2 noncoding 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; BRCA2 noncoding SNVs)	AUROC (zero-shot; BRCA2 noncoding SNVs)
SpliceAI (Evo 2 paper variant effect evaluations)Evaluation	0.89 (best in column)	0.939 (best in column)
CADD (Evo 2 paper variant effect evaluations)Evaluation	0.867	0.924
GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation	0.835	0.905
PhyloP 100 (Evo 2 paper variant effect evaluations)Evaluation	0.828	0.888
PhyloP 241 (Evo 2 paper variant effect evaluations)Evaluation	0.824	0.887
PhyloP 447 (Evo 2 paper variant effect evaluations)Evaluation	0.815	0.881
PhyloP 470 (Evo 2 paper variant effect evaluations)Evaluation	0.797	0.879
Evo 2 40B (Evo 2 paper variant effect evaluations)Evaluation	0.786	0.91
Evo 2 40B base (Evo 2 paper variant effect evaluations)Evaluation	0.784	0.903
Pangolin (Evo 2 paper variant effect evaluations)Evaluation	0.715	0.84
Evo 2 7B (Evo 2 paper variant effect evaluations)Evaluation	0.714	0.874
Evo 2 7B base (Evo 2 paper variant effect evaluations)Evaluation	0.703	0.873
NT (Evo 2 paper variant effect evaluations)Evaluation	0.361	0.555
RNA-FM (Evo 2 paper variant effect evaluations)Evaluation	0.312	0.54
Evo 1 (Evo 2 paper variant effect evaluations)Evaluation	0.265	0.545

All 30 result rows with coverage, uncertainty and sources

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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: CADD (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.867 AUPRC (zero-shot; BRCA2 noncoding 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 BRCA2 noncoding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-noncoding-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 J547, row 547: Model 'CADD', Data 'BRCA2', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: CADD (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.924 AUROC (zero-shot; BRCA2 noncoding 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 BRCA2 noncoding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-noncoding-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 I547, row 547: Model 'CADD', Data 'BRCA2', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 1 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.265 AUPRC (zero-shot; BRCA2 noncoding 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 BRCA2 noncoding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-noncoding-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 J559, row 559: Model 'Evo 1', Data 'BRCA2', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 1 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.545 AUROC (zero-shot; BRCA2 noncoding 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 BRCA2 noncoding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-noncoding-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 I559, row 559: Model 'Evo 1', Data 'BRCA2', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.784 AUPRC (zero-shot; BRCA2 noncoding 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 BRCA2 noncoding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-noncoding-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 J550, row 550: Model 'Evo 2 40B base', Data 'BRCA2', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.903 AUROC (zero-shot; BRCA2 noncoding 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 BRCA2 noncoding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-noncoding-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 I550, row 550: Model 'Evo 2 40B base', Data 'BRCA2', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.786 AUPRC (zero-shot; BRCA2 noncoding 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 BRCA2 noncoding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-noncoding-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 J548, row 548: Model 'Evo 2 40B', Data 'BRCA2', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.91 AUROC (zero-shot; BRCA2 noncoding 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 BRCA2 noncoding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-noncoding-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 I548, row 548: Model 'Evo 2 40B', Data 'BRCA2', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.703 AUPRC (zero-shot; BRCA2 noncoding 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 BRCA2 noncoding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-noncoding-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 J556, row 556: Model 'Evo 2 7B base', Data 'BRCA2', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.873 AUROC (zero-shot; BRCA2 noncoding 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 BRCA2 noncoding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-noncoding-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 I556, row 556: Model 'Evo 2 7B base', Data 'BRCA2', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.714 AUPRC (zero-shot; BRCA2 noncoding 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 BRCA2 noncoding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-noncoding-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 J555, row 555: Model 'Evo 2 7B', Data 'BRCA2', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.874 AUROC (zero-shot; BRCA2 noncoding 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 BRCA2 noncoding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-noncoding-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 I555, row 555: Model 'Evo 2 7B', Data 'BRCA2', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: GPN-MSA (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.835 AUPRC (zero-shot; BRCA2 noncoding 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 BRCA2 noncoding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-noncoding-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 J549, row 549: Model 'GPN-MSA', Data 'BRCA2', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: GPN-MSA (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.905 AUROC (zero-shot; BRCA2 noncoding 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 BRCA2 noncoding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-noncoding-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 I549, row 549: Model 'GPN-MSA', Data 'BRCA2', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.361 AUPRC (zero-shot; BRCA2 noncoding 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 BRCA2 noncoding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-noncoding-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 J558, row 558: Model 'NT', Data 'BRCA2', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.555 AUROC (zero-shot; BRCA2 noncoding 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 BRCA2 noncoding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-noncoding-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 I558, row 558: Model 'NT', Data 'BRCA2', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Pangolin (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.715 AUPRC (zero-shot; BRCA2 noncoding 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 BRCA2 noncoding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-noncoding-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 J557, row 557: Model 'Pangolin', Data 'BRCA2', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Pangolin (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.84 AUROC (zero-shot; BRCA2 noncoding 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 BRCA2 noncoding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-noncoding-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 I557, row 557: Model 'Pangolin', Data 'BRCA2', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.828 AUPRC (zero-shot; BRCA2 noncoding 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 BRCA2 noncoding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-noncoding-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 J551, row 551: Model 'PhyloP 100', Data 'BRCA2', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.888 AUROC (zero-shot; BRCA2 noncoding 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 BRCA2 noncoding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-noncoding-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 I551, row 551: Model 'PhyloP 100', Data 'BRCA2', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 241 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.824 AUPRC (zero-shot; BRCA2 noncoding 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 BRCA2 noncoding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-noncoding-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 J552, row 552: Model 'PhyloP 241', Data 'BRCA2', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: PhyloP 241 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.887 AUROC (zero-shot; BRCA2 noncoding 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 BRCA2 noncoding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-noncoding-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 I552, row 552: Model 'PhyloP 241', Data 'BRCA2', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 447 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.815 AUPRC (zero-shot; BRCA2 noncoding 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 BRCA2 noncoding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-noncoding-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 J553, row 553: Model 'PhyloP 447', Data 'BRCA2', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: PhyloP 447 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.881 AUROC (zero-shot; BRCA2 noncoding 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 BRCA2 noncoding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-noncoding-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 I553, row 553: Model 'PhyloP 447', Data 'BRCA2', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 470 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)	0.797 AUPRC (zero-shot; BRCA2 noncoding 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 470 on BRCA2 noncoding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca2-noncoding-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 J554, row 554: Model 'PhyloP 470', Data 'BRCA2', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

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Author-reported evaluations: 15

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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-brca2-noncoding-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 loss-of-function (P classes) versus functional (B classes) variants in the stratum Data 'BRCA2', Genomic_Feature 'Noncoding', Variant_Type 'SNV'.
version: As published, Nature 652 (2026), Supplementary Data 1
source locator: Supplementary Data 1 rows with Data 'BRCA2', Genomic_Feature 'Noncoding', Variant_Type 'SNV', Sub_category ''; SI A.3.12 and A.3.15 (pages 13 and 14)
limitations: Positives: 190 loss-of-function (P classes); negatives: 473 functional (B classes); total 663 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: BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026)
assessment: CADD on BRCA2 noncoding SNVs (Evo 2 paper)
assessment: Evo 1 on BRCA2 noncoding SNVs (Evo 2 paper)
assessment: Evo 2 40B base on BRCA2 noncoding SNVs (Evo 2 paper)
assessment: Evo 2 40B on BRCA2 noncoding SNVs (Evo 2 paper)
assessment: Evo 2 7B base on BRCA2 noncoding SNVs (Evo 2 paper)
assessment: Evo 2 7B on BRCA2 noncoding SNVs (Evo 2 paper)
assessment: GPN-MSA on BRCA2 noncoding SNVs (Evo 2 paper)
assessment: NT on BRCA2 noncoding SNVs (Evo 2 paper)
assessment: Pangolin on BRCA2 noncoding SNVs (Evo 2 paper)
assessment: PhyloP 100 on BRCA2 noncoding SNVs (Evo 2 paper)
assessment: PhyloP 241 on BRCA2 noncoding SNVs (Evo 2 paper)
assessment: PhyloP 447 on BRCA2 noncoding SNVs (Evo 2 paper)
assessment: PhyloP 470 on BRCA2 noncoding SNVs (Evo 2 paper)
assessment: RNA-FM on BRCA2 noncoding SNVs (Evo 2 paper)
assessment: SpliceAI on BRCA2 noncoding SNVs (Evo 2 paper)

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