Protocol

Zero-shot BRCA1 'Both' (coding and noncoding) 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 'Both' (coding and noncoding) SNVs stratum, AUROC and AUPRC.

15 evaluations · 30 results

Overview

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

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

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

View coverage and remaining gaps across all benchmarks

Results

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

All evaluations

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

Protocol: Zero-shot BRCA1 'Both' (coding and noncoding) 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 'Both' (coding and 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; BRCA1 'Both' (coding and noncoding) SNVs)	AUROC (zero-shot; BRCA1 'Both' (coding and noncoding) SNVs)
Evo 2 7B (Evo 2 paper variant effect evaluations)Evaluation	0.733 (best in column)	0.904 (best in column)
CADD (Evo 2 paper variant effect evaluations)Evaluation	0.73	0.876
Evo 2 7B base (Evo 2 paper variant effect evaluations)Evaluation	0.713	0.891
Evo 2 40B (Evo 2 paper variant effect evaluations)Evaluation	0.677	0.901
Evo 2 40B base (Evo 2 paper variant effect evaluations)Evaluation	0.673	0.897
GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation	0.65	0.863
PhyloP 447 (Evo 2 paper variant effect evaluations)Evaluation	0.54	0.821
PhyloP 241 (Evo 2 paper variant effect evaluations)Evaluation	0.532	0.811
SpliceAI (Evo 2 paper variant effect evaluations)Evaluation	0.508	0.686
PhyloP 100 (Evo 2 paper variant effect evaluations)Evaluation	0.495	0.811
PhyloP 470 (Evo 2 paper variant effect evaluations)Evaluation	0.481	0.807
Pangolin (Evo 2 paper variant effect evaluations)Evaluation	0.29	0.592
NT (Evo 2 paper variant effect evaluations)Evaluation	0.285	0.55
Evo 1 (Evo 2 paper variant effect evaluations)Evaluation	0.216	0.497
RNA-FM (Evo 2 paper variant effect evaluations)Evaluation	0.206	0.493

All 30 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: CADD (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.73 AUPRC (zero-shot; BRCA1 'Both' (coding and 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 BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-both-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 J608, row 608: Model 'CADD', Data 'BRCA1', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: CADD (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.876 AUROC (zero-shot; BRCA1 'Both' (coding and 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 BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-both-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 I608, row 608: Model 'CADD', Data 'BRCA1', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 1 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.216 AUPRC (zero-shot; BRCA1 'Both' (coding and 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 BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-both-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 J611, row 611: Model 'Evo 1', Data 'BRCA1', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 1 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.497 AUROC (zero-shot; BRCA1 'Both' (coding and 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 BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-both-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 I611, row 611: Model 'Evo 1', Data 'BRCA1', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.673 AUPRC (zero-shot; BRCA1 'Both' (coding and 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 BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-both-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 J617, row 617: Model 'Evo 2 40B base', Data 'BRCA1', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 40B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.897 AUROC (zero-shot; BRCA1 'Both' (coding and 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 BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-both-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 I617, row 617: Model 'Evo 2 40B base', Data 'BRCA1', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.677 AUPRC (zero-shot; BRCA1 'Both' (coding and 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 BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-both-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 J614, row 614: Model 'Evo 2 40B', Data 'BRCA1', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 40B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.901 AUROC (zero-shot; BRCA1 'Both' (coding and 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 BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-both-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 I614, row 614: Model 'Evo 2 40B', Data 'BRCA1', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.713 AUPRC (zero-shot; BRCA1 'Both' (coding and 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 BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-both-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 J623, row 623: Model 'Evo 2 7B base', Data 'BRCA1', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 7B base (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.891 AUROC (zero-shot; BRCA1 'Both' (coding and 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 BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-both-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 I623, row 623: Model 'Evo 2 7B base', Data 'BRCA1', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.733 AUPRC (zero-shot; BRCA1 'Both' (coding and 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 BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-both-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 J620, row 620: Model 'Evo 2 7B', Data 'BRCA1', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Evo 2 7B (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.904 AUROC (zero-shot; BRCA1 'Both' (coding and 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 BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-both-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 I620, row 620: Model 'Evo 2 7B', Data 'BRCA1', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: GPN-MSA (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.65 AUPRC (zero-shot; BRCA1 'Both' (coding and 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 BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-both-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 J626, row 626: Model 'GPN-MSA', Data 'BRCA1', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: GPN-MSA (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.863 AUROC (zero-shot; BRCA1 'Both' (coding and 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 BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-both-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 I626, row 626: Model 'GPN-MSA', Data 'BRCA1', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.285 AUPRC (zero-shot; BRCA1 'Both' (coding and 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 BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-both-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 J629, row 629: Model 'NT', Data 'BRCA1', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: NT (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.55 AUROC (zero-shot; BRCA1 'Both' (coding and 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 BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-both-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 I629, row 629: Model 'NT', Data 'BRCA1', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: Pangolin (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.29 AUPRC (zero-shot; BRCA1 'Both' (coding and 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 BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-both-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 J632, row 632: Model 'Pangolin', Data 'BRCA1', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: Pangolin (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.592 AUROC (zero-shot; BRCA1 'Both' (coding and 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 BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-both-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 I632, row 632: Model 'Pangolin', Data 'BRCA1', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.495 AUPRC (zero-shot; BRCA1 'Both' (coding and 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 BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-both-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 J635, row 635: Model 'PhyloP 100', Data 'BRCA1', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: PhyloP 100 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.811 AUROC (zero-shot; BRCA1 'Both' (coding and 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 BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-both-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 I635, row 635: Model 'PhyloP 100', Data 'BRCA1', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 241 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.532 AUPRC (zero-shot; BRCA1 'Both' (coding and 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 BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-both-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 J638, row 638: Model 'PhyloP 241', Data 'BRCA1', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: PhyloP 241 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.811 AUROC (zero-shot; BRCA1 'Both' (coding and 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 BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-both-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 I638, row 638: Model 'PhyloP 241', Data 'BRCA1', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 447 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.54 AUPRC (zero-shot; BRCA1 'Both' (coding and 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 BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-both-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 J641, row 641: Model 'PhyloP 447', Data 'BRCA1', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUPRC'
Configuration: PhyloP 447 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.821 AUROC (zero-shot; BRCA1 'Both' (coding and 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 BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-both-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 I641, row 641: Model 'PhyloP 447', Data 'BRCA1', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUROC'
Configuration: PhyloP 470 (Evo 2 paper variant effect evaluations)	Protocol: Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1) Dataset: BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026)	0.481 AUPRC (zero-shot; BRCA1 'Both' (coding and 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 BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper) gfm-guides-20261014-evo2-brixi2026-protocol-brca1-both-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 J644, row 644: Model 'PhyloP 470', Data 'BRCA1', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category '', column 'AUPRC'

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

Methods and evaluation design

Procedure, tasks and evaluated configurations

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Explore all linked results

Baseline coverage

Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.

0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.

No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.

Author-reported evaluations: 15

Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.

Null control

Proposed control: requires review

Protocol-valid seeded random ranking; no fitting on assay labels

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Conventional reference

Proposed control: requires review

Established label-free reference with explicitly permitted sequence/MSA inputs

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)

Coverage is derived from release 2026-10-22-1b7cf027e4f6. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

Run instructions

No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.

Strengths, limitations and unresolved questions

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

0 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance

No evidence rows match these filters. Choose another scope or clear the search.

How to read the evidence

Sources and history

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

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: gfm-guides-20261014-evo2-brixi2026-protocol-brca1-both-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 'Both', Variant_Type 'SNV'.
version: As published, Nature 652 (2026), Supplementary Data 1
source locator: Supplementary Data 1 rows with Data 'BRCA1', Genomic_Feature 'Both', Variant_Type 'SNV', Sub_category ''; SI A.3.12 and A.3.15 (pages 13 and 14); Extended Data Fig. 5a
limitations: Positives: 823 loss-of-function (LOF); negatives: 3070 functional or intermediate (FUNC, INT); total 3893 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: CADD on BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper)
assessment: Evo 1 on BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper)
assessment: Evo 2 40B base on BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper)
assessment: Evo 2 40B on BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper)
assessment: Evo 2 7B base on BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper)
assessment: Evo 2 7B on BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper)
assessment: GPN-MSA on BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper)
assessment: NT on BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper)
assessment: Pangolin on BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper)
assessment: PhyloP 100 on BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper)
assessment: PhyloP 241 on BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper)
assessment: PhyloP 447 on BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper)
assessment: PhyloP 470 on BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper)
assessment: RNA-FM on BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper)
assessment: SpliceAI on BRCA1 'Both' (coding and noncoding) SNVs (Evo 2 paper)

Suggest a correction