Protocol

Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1)

Zero-shot classification of loss-of-function (LOF) versus functional or intermediate (FUNC, INT) variants in the BRCA1 coding SNVs stratum, AUROC and AUPRC.

16 evaluations · 32 results

Overview

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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.

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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 BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1) · Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)

Sorted by AUPRC (zero-shot; BRCA1 coding 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; BRCA1 coding SNVs)	AUROC (zero-shot; BRCA1 coding SNVs)
AlphaMissense (Evo 2 paper variant effect evaluations)Evaluation	0.69 (best in column)	0.889 (best in column)
GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation	0.579	0.833
Evo 2 40B (Evo 2 paper variant effect evaluations)Evaluation	0.572	0.843
Evo 2 7B (Evo 2 paper variant effect evaluations)Evaluation	0.571	0.823
Evo 2 40B base (Evo 2 paper variant effect evaluations)Evaluation	0.559	0.83
Evo 2 7B base (Evo 2 paper variant effect evaluations)Evaluation	0.534	0.797
CADD (Evo 2 paper variant effect evaluations)Evaluation	0.521	0.814
PhyloP 447 (Evo 2 paper variant effect evaluations)Evaluation	0.471	0.785
PhyloP 100 (Evo 2 paper variant effect evaluations)Evaluation	0.454	0.781
PhyloP 241 (Evo 2 paper variant effect evaluations)Evaluation	0.437	0.759
PhyloP 470 (Evo 2 paper variant effect evaluations)Evaluation	0.436	0.774
SpliceAI (Evo 2 paper variant effect evaluations)Evaluation	0.284	0.55
Pangolin (Evo 2 paper variant effect evaluations)Evaluation	0.249	0.57
Evo 1 (Evo 2 paper variant effect evaluations)Evaluation	0.231	0.519
NT (Evo 2 paper variant effect evaluations)Evaluation	0.212	0.509
RNA-FM (Evo 2 paper variant effect evaluations)Evaluation	0.21	0.497

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 BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.69 AUPRC (zero-shot; BRCA1 coding 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 BRCA1 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-coding-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 J607, row 607: Model 'AlphaMissense', Data 'BRCA1', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: AlphaMissense (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.889 AUROC (zero-shot; BRCA1 coding 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 BRCA1 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-coding-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 I607, row 607: Model 'AlphaMissense', Data 'BRCA1', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: CADD (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.521 AUPRC (zero-shot; BRCA1 coding 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 BRCA1 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-coding-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 J609, row 609: Model 'CADD', Data 'BRCA1', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: CADD (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.814 AUROC (zero-shot; BRCA1 coding 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 BRCA1 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-coding-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 I609, row 609: Model 'CADD', Data 'BRCA1', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 1 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.231 AUPRC (zero-shot; BRCA1 coding 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 BRCA1 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-coding-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 J612, row 612: Model 'Evo 1', Data 'BRCA1', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 1 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.519 AUROC (zero-shot; BRCA1 coding 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 BRCA1 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-coding-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 I612, row 612: Model 'Evo 1', Data 'BRCA1', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.559 AUPRC (zero-shot; BRCA1 coding 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 BRCA1 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-coding-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 J618, row 618: Model 'Evo 2 40B base', Data 'BRCA1', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.83 AUROC (zero-shot; BRCA1 coding 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 BRCA1 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-coding-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 I618, row 618: Model 'Evo 2 40B base', Data 'BRCA1', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.572 AUPRC (zero-shot; BRCA1 coding 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 BRCA1 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-coding-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 J615, row 615: Model 'Evo 2 40B', Data 'BRCA1', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.843 AUROC (zero-shot; BRCA1 coding 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 BRCA1 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-coding-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 I615, row 615: Model 'Evo 2 40B', Data 'BRCA1', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.534 AUPRC (zero-shot; BRCA1 coding 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 BRCA1 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-coding-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 J624, row 624: Model 'Evo 2 7B base', Data 'BRCA1', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.797 AUROC (zero-shot; BRCA1 coding 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 BRCA1 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-coding-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 I624, row 624: Model 'Evo 2 7B base', Data 'BRCA1', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.571 AUPRC (zero-shot; BRCA1 coding 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 BRCA1 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-coding-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 J621, row 621: Model 'Evo 2 7B', Data 'BRCA1', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.823 AUROC (zero-shot; BRCA1 coding 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 BRCA1 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-coding-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 I621, row 621: Model 'Evo 2 7B', Data 'BRCA1', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: GPN-MSA (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.579 AUPRC (zero-shot; BRCA1 coding 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 BRCA1 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-coding-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 J627, row 627: Model 'GPN-MSA', Data 'BRCA1', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: GPN-MSA (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.833 AUROC (zero-shot; BRCA1 coding 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 BRCA1 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-coding-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 I627, row 627: Model 'GPN-MSA', Data 'BRCA1', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.212 AUPRC (zero-shot; BRCA1 coding 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 BRCA1 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-coding-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 J630, row 630: Model 'NT', Data 'BRCA1', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.509 AUROC (zero-shot; BRCA1 coding 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 BRCA1 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-coding-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 I630, row 630: Model 'NT', Data 'BRCA1', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Pangolin (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.249 AUPRC (zero-shot; BRCA1 coding 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 BRCA1 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-coding-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 J633, row 633: Model 'Pangolin', Data 'BRCA1', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Pangolin (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.57 AUROC (zero-shot; BRCA1 coding 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 BRCA1 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-coding-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 I633, row 633: Model 'Pangolin', Data 'BRCA1', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.454 AUPRC (zero-shot; BRCA1 coding 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 BRCA1 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-coding-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 J636, row 636: Model 'PhyloP 100', Data 'BRCA1', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.781 AUROC (zero-shot; BRCA1 coding 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 BRCA1 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-coding-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 I636, row 636: Model 'PhyloP 100', Data 'BRCA1', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 241 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.437 AUPRC (zero-shot; BRCA1 coding 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 BRCA1 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-coding-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 J639, row 639: Model 'PhyloP 241', Data 'BRCA1', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: PhyloP 241 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.759 AUROC (zero-shot; BRCA1 coding 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 BRCA1 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-coding-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 I639, row 639: Model 'PhyloP 241', Data 'BRCA1', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 447 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.471 AUPRC (zero-shot; BRCA1 coding 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 BRCA1 coding SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-coding-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 J642, row 642: Model 'PhyloP 447', Data 'BRCA1', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category '', column 'AUPRC'

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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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Stable ID: gfm-guides-20261014-evo2-brixi2026-protocol-brca1-coding-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 (LOF) versus functional or intermediate (FUNC, INT) variants in the stratum Data 'BRCA1', Genomic_Feature 'Coding', Variant_Type 'SNV'.
version: As published, Nature 652 (2026), Supplementary Data 1
source locator: Supplementary Data 1 rows with Data 'BRCA1', Genomic_Feature 'Coding', Variant_Type 'SNV', Sub_category ''; SI A.3.12 and A.3.15 (pages 13 and 14); Fig. 3e
limitations: Positives: 584 loss-of-function (LOF); negatives: 2184 functional or intermediate (FUNC, INT); total 2768 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: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)
assessment: AlphaMissense on BRCA1 coding SNVs (Evo 2 paper)
assessment: CADD on BRCA1 coding SNVs (Evo 2 paper)
assessment: Evo 1 on BRCA1 coding SNVs (Evo 2 paper)
assessment: Evo 2 40B base on BRCA1 coding SNVs (Evo 2 paper)
assessment: Evo 2 40B on BRCA1 coding SNVs (Evo 2 paper)
assessment: Evo 2 7B base on BRCA1 coding SNVs (Evo 2 paper)
assessment: Evo 2 7B on BRCA1 coding SNVs (Evo 2 paper)
assessment: GPN-MSA on BRCA1 coding SNVs (Evo 2 paper)
assessment: NT on BRCA1 coding SNVs (Evo 2 paper)
assessment: Pangolin on BRCA1 coding SNVs (Evo 2 paper)
assessment: PhyloP 100 on BRCA1 coding SNVs (Evo 2 paper)
assessment: PhyloP 241 on BRCA1 coding SNVs (Evo 2 paper)
assessment: PhyloP 447 on BRCA1 coding SNVs (Evo 2 paper)
assessment: PhyloP 470 on BRCA1 coding SNVs (Evo 2 paper)
assessment: RNA-FM on BRCA1 coding SNVs (Evo 2 paper)
assessment: SpliceAI on BRCA1 coding SNVs (Evo 2 paper)

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