Dataset

Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas)

Saturation genome editing variant effect measurements for BRCA1 (two studies), BRCA2, BAP1, RAD51C, VHL, DDX3X, RNU4-2, ATM, BARD1, PALB2, XRCC2, SFPQ and CTCF, with author thresholds defining functionally normal versus abnormal variants.

Evaluation results

26 evaluations · 26 results. Different protocols are not a single leaderboard.

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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: AVI six-model ensemble (AlphaGenome Atlas v1)	Protocol: SGE held-out screens pooled, SNVs and indels, AUPRC (AlphaGenome Atlas) Dataset: Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas)	0.759 AUPRC (pooled held-out SGE screens, functionally abnormal vs normal, SNVs and indels) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI on pooled held-out SGE screens, all-variants (AlphaGenome Atlas fig. S7F) ag-atlas-20261019-protocol-sge-pooled-all-variants-auprc Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · fig. S7F (left) legend entry 'AVI (AUPRC = 0.759)' (page 57)
Configuration: Zoonomia Cactus 241-way phyloP (AlphaGenome Atlas v1)	Protocol: SGE held-out screens pooled, SNVs and indels, AUPRC (AlphaGenome Atlas) Dataset: Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas)	0.408 AUPRC (pooled held-out SGE screens, functionally abnormal vs normal, SNVs and indels) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Cactus 241-way on pooled held-out SGE screens, all-variants (AlphaGenome Atlas fig. S7F) ag-atlas-20261019-protocol-sge-pooled-all-variants-auprc Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · fig. S7F (left) legend entry 'Cactus 241-way (AUPRC = 0.408)' (page 57)
Configuration: CADD v1.7 GRCh38, precomputed plus pipeline for missing indels (AlphaGenome Atlas v1)	Protocol: SGE held-out screens pooled, SNVs and indels, AUPRC (AlphaGenome Atlas) Dataset: Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas)	0.653 AUPRC (pooled held-out SGE screens, functionally abnormal vs normal, SNVs and indels) 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 v1.7 on pooled held-out SGE screens, all-variants (AlphaGenome Atlas fig. S7F) ag-atlas-20261019-protocol-sge-pooled-all-variants-auprc Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · fig. S7F (left) legend entry 'CADD v1.7 (AUPRC = 0.653)' (page 57)
Configuration: gnomAD v4.1 genome allele frequency, negated (AlphaGenome Atlas v1)	Protocol: SGE held-out screens pooled, SNVs and indels, AUPRC (AlphaGenome Atlas) Dataset: Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas)	0.2 AUPRC (pooled held-out SGE screens, functionally abnormal vs normal, SNVs and indels) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source gnomAD allele frequency on pooled held-out SGE screens, all-variants (AlphaGenome Atlas fig. S7F) ag-atlas-20261019-protocol-sge-pooled-all-variants-auprc Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · fig. S7F (left) legend entry 'gnomAD allele frequency (AUPRC = 0.200)' (page 57)
Configuration: PhastCons 470-way (AlphaGenome Atlas v1)	Protocol: SGE held-out screens pooled, SNVs and indels, AUPRC (AlphaGenome Atlas) Dataset: Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas)	0.316 AUPRC (pooled held-out SGE screens, functionally abnormal vs normal, SNVs and indels) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Phastcons 470-way on pooled held-out SGE screens, all-variants (AlphaGenome Atlas fig. S7F) ag-atlas-20261019-protocol-sge-pooled-all-variants-auprc Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · fig. S7F (left) legend entry 'Phastcons 470-way (AUPRC = 0.316)' (page 57)
Configuration: AVI six-model ensemble (AlphaGenome Atlas v1)	Protocol: SGE held-out screens pooled, functionally abnormal versus normal SNVs, AUPRC (AlphaGenome Atlas) Dataset: Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas)	0.668 AUPRC (pooled held-out SGE screens, functionally abnormal vs normal, SNVs only) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI on pooled held-out SGE screens, snv (AlphaGenome Atlas fig. S7E) ag-atlas-20261019-protocol-sge-pooled-snv-auprc Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · fig. S7E (left) legend entry 'AVI (AUPRC = 0.668)' (page 57)
Configuration: Zoonomia Cactus 241-way phyloP (AlphaGenome Atlas v1)	Protocol: SGE held-out screens pooled, functionally abnormal versus normal SNVs, AUPRC (AlphaGenome Atlas) Dataset: Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas)	0.296 AUPRC (pooled held-out SGE screens, functionally abnormal vs normal, SNVs only) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Cactus 241-way on pooled held-out SGE screens, snv (AlphaGenome Atlas fig. S7E) ag-atlas-20261019-protocol-sge-pooled-snv-auprc Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · fig. S7E (left) legend entry 'Cactus 241-way (AUPRC = 0.296)' (page 57)
Configuration: CADD v1.7 GRCh38, precomputed plus pipeline for missing indels (AlphaGenome Atlas v1)	Protocol: SGE held-out screens pooled, functionally abnormal versus normal SNVs, AUPRC (AlphaGenome Atlas) Dataset: Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas)	0.647 AUPRC (pooled held-out SGE screens, functionally abnormal vs normal, SNVs only) 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 v1.7 on pooled held-out SGE screens, snv (AlphaGenome Atlas fig. S7E) ag-atlas-20261019-protocol-sge-pooled-snv-auprc Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · fig. S7E (left) legend entry 'CADD v1.7 (AUPRC = 0.647)' (page 57)
Configuration: gnomAD v4.1 genome allele frequency, negated (AlphaGenome Atlas v1)	Protocol: SGE held-out screens pooled, functionally abnormal versus normal SNVs, AUPRC (AlphaGenome Atlas) Dataset: Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas)	0.15 AUPRC (pooled held-out SGE screens, functionally abnormal vs normal, SNVs only) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source gnomAD allele frequency on pooled held-out SGE screens, snv (AlphaGenome Atlas fig. S7E) ag-atlas-20261019-protocol-sge-pooled-snv-auprc Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · fig. S7E (left) legend entry 'gnomAD allele frequency (AUPRC = 0.150)' (page 57)
Configuration: GPN-Star (M), mammalian, mutation-rate calibrated (AlphaGenome Atlas v1)	Protocol: SGE held-out screens pooled, functionally abnormal versus normal SNVs, AUPRC (AlphaGenome Atlas) Dataset: Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas)	0.398 AUPRC (pooled held-out SGE screens, functionally abnormal vs normal, SNVs only) 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 STAR (M) on pooled held-out SGE screens, snv (AlphaGenome Atlas fig. S7E) ag-atlas-20261019-protocol-sge-pooled-snv-auprc Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · fig. S7E (left) legend entry 'GPN STAR (M) (AUPRC = 0.398)' (page 57)
Configuration: GPN-Star (V), vertebrate, mutation-rate calibrated (AlphaGenome Atlas v1)	Protocol: SGE held-out screens pooled, functionally abnormal versus normal SNVs, AUPRC (AlphaGenome Atlas) Dataset: Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas)	0.425 AUPRC (pooled held-out SGE screens, functionally abnormal vs normal, SNVs only) 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 STAR (V) on pooled held-out SGE screens, snv (AlphaGenome Atlas fig. S7E) ag-atlas-20261019-protocol-sge-pooled-snv-auprc Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · fig. S7E (left) legend entry 'GPN STAR (V) (AUPRC = 0.425)' (page 57)
Configuration: PhastCons 470-way (AlphaGenome Atlas v1)	Protocol: SGE held-out screens pooled, functionally abnormal versus normal SNVs, AUPRC (AlphaGenome Atlas) Dataset: Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas)	0.236 AUPRC (pooled held-out SGE screens, functionally abnormal vs normal, SNVs only) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Phastcons 470-way on pooled held-out SGE screens, snv (AlphaGenome Atlas fig. S7E) ag-atlas-20261019-protocol-sge-pooled-snv-auprc Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · fig. S7E (left) legend entry 'Phastcons 470-way (AUPRC = 0.236)' (page 57)
Configuration: AVI six-model ensemble (AlphaGenome Atlas v1)	Protocol: AVI feature ablation, SGE column, AUPRC (AlphaGenome Atlas Table S2) Dataset: Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas)	0.731 AUPRC (AVI baseline row, SGE column) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI AVI Model (Baseline) on SGE (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-sge Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Baseline', row 'AVI Model', column 'SGE'
Configuration: AVI ablation 'All except AlphaGenome' (Retrained, AlphaGenome Atlas Table S2)	Protocol: AVI feature ablation, SGE column, AUPRC (AlphaGenome Atlas Table S2) Dataset: Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas)	-47.1% AUPRC relative difference (ablation 'All except AlphaGenome' (Retrained) relative to the AVI baseline row, SGE column) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI All except AlphaGenome (Retrained) on SGE (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-sge Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Retrained', row 'All except AlphaGenome', column 'SGE'
Configuration: AVI ablation 'AlphaGenome' (Retrained, AlphaGenome Atlas Table S2)	Protocol: AVI feature ablation, SGE column, AUPRC (AlphaGenome Atlas Table S2) Dataset: Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas)	-8.29% AUPRC relative difference (ablation 'AlphaGenome' (Retrained) relative to the AVI baseline row, SGE column) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI AlphaGenome (Retrained) on SGE (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-sge Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Retrained', row 'AlphaGenome', column 'SGE'
Configuration: AVI ablation 'AlphaMissense' (Retrained, AlphaGenome Atlas Table S2)	Protocol: AVI feature ablation, SGE column, AUPRC (AlphaGenome Atlas Table S2) Dataset: Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas)	-0.45% AUPRC relative difference (ablation 'AlphaMissense' (Retrained) relative to the AVI baseline row, SGE column) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI AlphaMissense (Retrained) on SGE (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-sge Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Retrained', row 'AlphaMissense', column 'SGE'
Configuration: AVI ablation 'Cactus' (Retrained, AlphaGenome Atlas Table S2)	Protocol: AVI feature ablation, SGE column, AUPRC (AlphaGenome Atlas Table S2) Dataset: Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas)	-1.32% AUPRC relative difference (ablation 'Cactus' (Retrained) relative to the AVI baseline row, SGE column) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI Cactus (Retrained) on SGE (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-sge Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Retrained', row 'Cactus', column 'SGE'
Configuration: AVI ablation 'Consequence' (Retrained, AlphaGenome Atlas Table S2)	Protocol: AVI feature ablation, SGE column, AUPRC (AlphaGenome Atlas Table S2) Dataset: Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas)	-27.4% AUPRC relative difference (ablation 'Consequence' (Retrained) relative to the AVI baseline row, SGE column) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI Consequence (Retrained) on SGE (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-sge Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Retrained', row 'Consequence', column 'SGE'
Configuration: AVI ablation 'Conservation' (Retrained, AlphaGenome Atlas Table S2)	Protocol: AVI feature ablation, SGE column, AUPRC (AlphaGenome Atlas Table S2) Dataset: Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas)	-2.36% AUPRC relative difference (ablation 'Conservation' (Retrained) relative to the AVI baseline row, SGE column) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI Conservation (Retrained) on SGE (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-sge Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Retrained', row 'Conservation', column 'SGE'
Configuration: AVI ablation 'Indel Type' (Retrained, AlphaGenome Atlas Table S2)	Protocol: AVI feature ablation, SGE column, AUPRC (AlphaGenome Atlas Table S2) Dataset: Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas)	0.08% AUPRC relative difference (ablation 'Indel Type' (Retrained) relative to the AVI baseline row, SGE column) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI Indel Type (Retrained) on SGE (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-sge Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Retrained', row 'Indel Type', column 'SGE'
Configuration: AVI ablation 'PhastCons' (Retrained, AlphaGenome Atlas Table S2)	Protocol: AVI feature ablation, SGE column, AUPRC (AlphaGenome Atlas Table S2) Dataset: Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas)	-5.2% AUPRC relative difference (ablation 'PhastCons' (Retrained) relative to the AVI baseline row, SGE column) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI PhastCons (Retrained) on SGE (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-sge Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Retrained', row 'PhastCons', column 'SGE'
Configuration: AVI ablation 'Protein' (Retrained, AlphaGenome Atlas Table S2)	Protocol: AVI feature ablation, SGE column, AUPRC (AlphaGenome Atlas Table S2) Dataset: Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas)	-23.8% AUPRC relative difference (ablation 'Protein' (Retrained) relative to the AVI baseline row, SGE column) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI Protein (Retrained) on SGE (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-sge Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Retrained', row 'Protein', column 'SGE'
Configuration: AVI ablation 'Splicing Removed Only' (Retrained, AlphaGenome Atlas Table S2)	Protocol: AVI feature ablation, SGE column, AUPRC (AlphaGenome Atlas Table S2) Dataset: Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas)	-7.46% AUPRC relative difference (ablation 'Splicing Removed Only' (Retrained) relative to the AVI baseline row, SGE column) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI Splicing Removed Only (Retrained) on SGE (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-sge Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Retrained', row 'Splicing Removed Only', column 'SGE'
Configuration: AVI ablation '+ No Indel Type' (Features Set to Zero, AlphaGenome Atlas Table S2)	Protocol: AVI feature ablation, SGE column, AUPRC (AlphaGenome Atlas Table S2) Dataset: Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas)	-5.14% AUPRC relative difference (ablation '+ No Indel Type (second occurrence, below 'No AlphaMissense Indel Features')' (Features Set to Zero) relative to the AVI baseline row, SGE column) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI + No Indel Type (Features Set to Zero) on SGE (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-sge Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Features Set to Zero', row '+ No Indel Type (second occurrence, below 'No AlphaMissense Indel Features')', column 'SGE'
Configuration: AVI ablation 'No AlphaMissense Indel Features' (Features Set to Zero, AlphaGenome Atlas Table S2)	Protocol: AVI feature ablation, SGE column, AUPRC (AlphaGenome Atlas Table S2) Dataset: Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas)	-4.14% AUPRC relative difference (ablation 'No AlphaMissense Indel Features' (Features Set to Zero) relative to the AVI baseline row, SGE column) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI No AlphaMissense Indel Features (Features Set to Zero) on SGE (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-sge Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Features Set to Zero', row 'No AlphaMissense Indel Features', column 'SGE'

Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.

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Readiness checks, gaps and artifacts

Release 2026-11-02-a7f03c9e55a5 · Evidence verified: Not verified

Evidence incomplete

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Verified: Not verified

Evidence incomplete

Investigate discrepancies

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Missing or unresolved evidence

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File checksums match the recorded files: not yet verified
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Score meaning and direction are confirmed: not yet verified
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Verified: Not verified

Evidence incomplete

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Missing or unresolved evidence

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Verified: Not verified

Evidence incomplete

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Evidence

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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.

4 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statement	Original source and location	Review and provenance
Source location Methods 'Saturation Genome Editing (SGE)' (pages 27 to 28) Context-only references	AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) Original source ↗ Methods 'Saturation Genome Editing (SGE)' (pages 27 to 28) Version: medRxiv preprint version 1, posted 2026-09-20; full-text PDF with supplementary figures and tables (83 pages) Retrieved: 2026-10-19T12:19:03Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `b32d1539005ca4ea31c3dcef49b834424b1d8b5da4ce6b9fc3e1f942d39fc453` Hash scope: SHA-256 of one retrieval of the medRxiv PDF. A second retrieval at 2026-10-19T12:30:54Z had the same length (15,415,633 bytes) and the same SHA-256. Inspected artifact
Split Four studies (FINDLAY_2018_BRCA1, LEE_2025_ATM, OLVERA_LEON_2024_RAD51C, RADFORD_2023_DDX3X) used for online validation during AVI training; the other ten held out as test, with AVI positional filtering. Variants in 'uncertain' or 'intermediate' classes removed. Context-only references	AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) Original source ↗ Methods 'Saturation Genome Editing (SGE)' (pages 27 to 28) Version: medRxiv preprint version 1, posted 2026-09-20; full-text PDF with supplementary figures and tables (83 pages) Retrieved: 2026-10-19T12:19:03Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.split` Source artifact SHA-256: `b32d1539005ca4ea31c3dcef49b834424b1d8b5da4ce6b9fc3e1f942d39fc453` Hash scope: SHA-256 of one retrieval of the medRxiv PDF. A second retrieval at 2026-10-19T12:30:54Z had the same length (15,415,633 bytes) and the same SHA-256. Inspected artifact
Description Saturation genome editing variant effect measurements for BRCA1 (two studies), BRCA2, BAP1, RAD51C, VHL, DDX3X, RNU4-2, ATM, BARD1, PALB2, XRCC2, SFPQ and CTCF, with author thresholds defining functionally normal versus abnormal variants. Context-only references	AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) Original source ↗ Methods 'Saturation Genome Editing (SGE)' (pages 27 to 28) Version: medRxiv preprint version 1, posted 2026-09-20; full-text PDF with supplementary figures and tables (83 pages) Retrieved: 2026-10-19T12:19:03Z	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `b32d1539005ca4ea31c3dcef49b834424b1d8b5da4ce6b9fc3e1f942d39fc453` Hash scope: SHA-256 of one retrieval of the medRxiv PDF. A second retrieval at 2026-10-19T12:30:54Z had the same length (15,415,633 bytes) and the same SHA-256. Inspected artifact
Name Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas) Context-only references	AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) Original source ↗ Methods 'Saturation Genome Editing (SGE)' (pages 27 to 28) Version: medRxiv preprint version 1, posted 2026-09-20; full-text PDF with supplementary figures and tables (83 pages) Retrieved: 2026-10-19T12:19:03Z	not individually reviewed No individual claim review recorded Audit details Field: `name` Source artifact SHA-256: `b32d1539005ca4ea31c3dcef49b834424b1d8b5da4ce6b9fc3e1f942d39fc453` Hash scope: SHA-256 of one retrieval of the medRxiv PDF. A second retrieval at 2026-10-19T12:30:54Z had the same length (15,415,633 bytes) and the same SHA-256. Inspected artifact

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Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

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AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Original source · medRxiv preprint version 1, posted 2026-09-20; full-text PDF with supplementary figures and tables (83 pages)

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Stable ID: ag-atlas-20261019-data-sge-screens

areas: dna-genomes
contexts: research
split: Four studies (FINDLAY_2018_BRCA1, LEE_2025_ATM, OLVERA_LEON_2024_RAD51C, RADFORD_2023_DDX3X) used for online validation during AVI training; the other ten held out as test, with AVI positional filtering. Variants in 'uncertain' or 'intermediate' classes removed.
source locator: Methods 'Saturation Genome Editing (SGE)' (pages 27 to 28)

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