CADD v1.7 GRCh38, precomputed plus pipeline for missing indels (AlphaGenome Atlas v1); v1.7 (GRCh38)

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Evaluations and results

6 evaluations · 6 results. Different protocols are not a single leaderboard.

Sorted by AUPRC (ClinVar pathogenic vs benign SNVs, Synonymous) (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	Protocol and dataset	AUPRC (ClinVar pathogenic vs benign SNVs, Synonymous)	AUPRC (pooled held-out SGE screens, functionally abnormal vs normal, SNVs and indels)	AUPRC (pooled held-out SGE screens, functionally abnormal vs normal, SNVs only)	Average precision (DNM1 minigene screen, active vs inactive variants)	Recall (known P/LP variants ranked within the top 50 of each patient's variants; 105 causal variants, background filtered at gnomAD AF 0.001)	Recall (known P/LP variants ranked within the top 50 of each patient's variants; 112 causal variants, all patient variants)
CADD v1.7 GRCh38, precomputed plus pipeline for missing indels (AlphaGenome Atlas v1)Evaluation	ClinVar pathogenic versus benign SNVs by VEP consequence, AUPRC (AlphaGenome Atlas), ClinVar 2025-06-15 SNVs, Synonymous (AlphaGenome Atlas test set)	0.35	Not reported	Not reported	Not reported	Not reported	Not reported
CADD v1.7 GRCh38, precomputed plus pipeline for missing indels (AlphaGenome Atlas v1)Evaluation	DNM1 minigene screen, active versus inactive variants, average precision (AlphaGenome Atlas), DNM1 intron saturation mutagenesis minigene splicing screen (AlphaGenome Atlas Data S1)	Not reported	Not reported	Not reported	0.289	Not reported	Not reported
CADD v1.7 GRCh38, precomputed plus pipeline for missing indels (AlphaGenome Atlas v1)Evaluation	GREGoR solved cases, recall of causal variants in the top 50 per patient (AlphaGenome Atlas), GREGoR solved rare disease cases, likely pathogenic and pathogenic variants (AlphaGenome Atlas)	Not reported	Not reported	Not reported	Not reported	61%	Not reported
CADD v1.7 GRCh38, precomputed plus pipeline for missing indels (AlphaGenome Atlas v1)Evaluation	GREGoR solved cases, recall of causal variants in the top 50 per patient (AlphaGenome Atlas), GREGoR solved rare disease cases, likely pathogenic and pathogenic variants (AlphaGenome Atlas)	Not reported	Not reported	Not reported	Not reported	Not reported	12.5%
CADD v1.7 GRCh38, precomputed plus pipeline for missing indels (AlphaGenome Atlas v1)Evaluation	SGE held-out screens pooled, SNVs and indels, AUPRC (AlphaGenome Atlas), Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas)	Not reported	0.653	Not reported	Not reported	Not reported	Not reported
CADD v1.7 GRCh38, precomputed plus pipeline for missing indels (AlphaGenome Atlas v1)Evaluation	SGE held-out screens pooled, functionally abnormal versus normal SNVs, AUPRC (AlphaGenome Atlas), Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas)	Not reported	Not reported	0.647	Not reported	Not reported	Not reported

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: CADD v1.7 GRCh38, precomputed plus pipeline for missing indels (AlphaGenome Atlas v1)	Protocol: ClinVar pathogenic versus benign SNVs by VEP consequence, AUPRC (AlphaGenome Atlas) Dataset subset: ClinVar 2025-06-15 SNVs, Synonymous (AlphaGenome Atlas test set)	0.35 AUPRC (ClinVar pathogenic vs benign SNVs, Synonymous) unitless · higher Uncertainty: Not reported by the source: Fig. 2A draws 95% bootstrap intervals (100 bootstraps) without printing them. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source cadd-v1-7 on ClinVar Synonymous SNVs (AlphaGenome Atlas Fig. 2A) ag-atlas-20261019-protocol-clinvar-snv-by-consequence-auprc Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Results 'State-of-the-art interpretable genome-wide variant prioritization with AVI' paragraph 1 (page 5), citing Fig. 2A: 'synonymous (0.57 vs. CADD v1.7’s 0.35)'
Configuration: CADD v1.7 GRCh38, precomputed plus pipeline for missing indels (AlphaGenome Atlas v1)	Protocol: DNM1 minigene screen, active versus inactive variants, average precision (AlphaGenome Atlas) Dataset: DNM1 intron saturation mutagenesis minigene splicing screen (AlphaGenome Atlas Data S1)	0.289 Average precision (DNM1 minigene screen, active vs inactive variants) 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 PHRED on the DNM1 minigene splicing screen (AlphaGenome Atlas fig. S9E) ag-atlas-20261019-protocol-dnm1-active-variant-ap Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · fig. S9E legend entry 'CADD PHRED (AP=0.289)' (page 60)
Configuration: CADD v1.7 GRCh38, precomputed plus pipeline for missing indels (AlphaGenome Atlas v1)	Protocol: GREGoR solved cases, recall of causal variants in the top 50 per patient (AlphaGenome Atlas) Dataset: GREGoR solved rare disease cases, likely pathogenic and pathogenic variants (AlphaGenome Atlas)	61% Recall (known P/LP variants ranked within the top 50 of each patient's variants; 105 causal variants, background filtered at gnomAD AF 0.001) percent · 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 GREGoR solved cases, af-filtered (AlphaGenome Atlas) ag-atlas-20261019-protocol-gregor-recall-top50 Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Results 'AVI prioritization helped resolve a rare disease case...' paragraph 1 (page 7)
Configuration: CADD v1.7 GRCh38, precomputed plus pipeline for missing indels (AlphaGenome Atlas v1)	Protocol: GREGoR solved cases, recall of causal variants in the top 50 per patient (AlphaGenome Atlas) Dataset: GREGoR solved rare disease cases, likely pathogenic and pathogenic variants (AlphaGenome Atlas)	12.5% Recall (known P/LP variants ranked within the top 50 of each patient's variants; 112 causal variants, all patient variants) percent · 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 GREGoR solved cases, all-variants (AlphaGenome Atlas) ag-atlas-20261019-protocol-gregor-recall-top50 Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Results 'AVI prioritization helped resolve a rare disease case...' paragraph 1 (page 7)
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: 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)

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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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Technical metadata and extraction receipts

Stable ID: ag-atlas-20261019-config-cadd-v1-7

areas: dna-genomes
contexts: research
method types: conventional_pipeline
reported name: CADD v1.7
version: v1.7 (GRCh38)
source locator: Methods 'Obtaining baseline scores' (pages 26 to 27)

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