Rare gnomAD missense variants in genes with at least one ClinVar pathogenic variant, used to estimate the prior probability of pathogenicity (4.41%) and to count how often each evidence strength is assigned.
3 evaluations · 3 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: CADD (Pejaver et al. 2022 calibration) | Protocol: Share of gnomAD variants called pathogenic at developer thresholds (Pejaver et al. 2022 Table 3) Dataset: gnomAD reference set (Pejaver et al. 2022) | 0.651 Proportion (gnomAD-set variants predicted pathogenic at the developer threshold) fraction · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCADD at developer threshold 20.000: gnomAD fraction called pathogenic (Pejaver et al. 2022) vep-uc-20261014-protocol-pejaver2022-developer-threshold-gnomad-fraction Aggregation: Not reported Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) · Table 3, row 'CADD', column 'Fraction of predicted pathogenic variants in the gnomAD set' |
| Configuration: PolyPhen-2 (Pejaver et al. 2022 calibration) | Protocol: Share of gnomAD variants called pathogenic at developer thresholds (Pejaver et al. 2022 Table 3) Dataset: gnomAD reference set (Pejaver et al. 2022) | 0.293 Proportion (gnomAD-set variants predicted pathogenic at the developer threshold) fraction · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcePolyPhen-2 at developer threshold 0.902: gnomAD fraction called pathogenic (Pejaver et al. 2022) vep-uc-20261014-protocol-pejaver2022-developer-threshold-gnomad-fraction Aggregation: Not reported Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) · Table 3, row 'PolyPhen-2', column 'Fraction of predicted pathogenic variants in the gnomAD set' |
| Configuration: SIFT (Pejaver et al. 2022 calibration) | Protocol: Share of gnomAD variants called pathogenic at developer thresholds (Pejaver et al. 2022 Table 3) Dataset: gnomAD reference set (Pejaver et al. 2022) | 0.504 Proportion (gnomAD-set variants predicted pathogenic at the developer threshold) fraction · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSIFT at developer threshold 0.050: gnomAD fraction called pathogenic (Pejaver et al. 2022) vep-uc-20261014-protocol-pejaver2022-developer-threshold-gnomad-fraction Aggregation: Not reported Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) · Table 3, row 'SIFT', column 'Fraction of predicted pathogenic variants in the gnomAD set' |
Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.
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9 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Access Supplementary Data S2 (Excel), not retrieved in this pass. Context-only references | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Methods 'The gnomAD set' and 'Estimation of the prevalence of pathogenic variants'; Figure 1B Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact downloaded bytes, before optional gzip storage |
| Label semantics Unlabelled reference population; used for the prior and for the fraction of variants assigned each strength. Context-only references | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Methods 'The gnomAD set' and 'Estimation of the prevalence of pathogenic variants'; Figure 1B Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact downloaded bytes, before optional gzip storage |
| Population 363,894 variants from 3,640 genes after quality, segmental-duplication and training-set filters and removal of variants in ClinVar (December 2019). Context-only references | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Methods 'The gnomAD set' and 'Estimation of the prevalence of pathogenic variants'; Figure 1B Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact downloaded bytes, before optional gzip storage |
| Source location Methods 'The gnomAD set' and 'Estimation of the prevalence of pathogenic variants'; Figure 1B Context-only references | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Methods 'The gnomAD set' and 'Estimation of the prevalence of pathogenic variants'; Figure 1B Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact downloaded bytes, before optional gzip storage |
| Species Homo sapiens Context-only references | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Methods 'The gnomAD set' and 'Estimation of the prevalence of pathogenic variants'; Figure 1B Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact downloaded bytes, before optional gzip storage |
| Split Whole set; not a labelled test set Context-only references | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Methods 'The gnomAD set' and 'Estimation of the prevalence of pathogenic variants'; Figure 1B Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact downloaded bytes, before optional gzip storage |
| Version gnomAD v2.1 exomes and genomes, filtered as in Figure 1B Context-only references | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Methods 'The gnomAD set' and 'Estimation of the prevalence of pathogenic variants'; Figure 1B Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact downloaded bytes, before optional gzip storage |
| Description Rare gnomAD missense variants in genes with at least one ClinVar pathogenic variant, used to estimate the prior probability of pathogenicity (4.41%) and to count how often each evidence strength is assigned. Context-only references | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Methods 'The gnomAD set' and 'Estimation of the prevalence of pathogenic variants'; Figure 1B Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact downloaded bytes, before optional gzip storage |
| Name gnomAD reference set (Pejaver et al. 2022) Context-only references | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Methods 'The gnomAD set' and 'Estimation of the prevalence of pathogenic variants'; Figure 1B Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact downloaded bytes, before optional gzip storage |
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
Stable ID: vep-uc-20261014-dataset-pejaver2022-gnomad