Configuration

PhD-SNPg-p005 (Cubuk et al. 2021)

PhD-SNPg scores dichotomised at the cited threshold.

Overview

PhD-SNPg scores dichotomised at the cited threshold.

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

Evaluations and results

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

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: PhD-SNPg-p005 (Cubuk et al. 2021)	Protocol: BRCA1 functional truth set, binary in silico calls (Cubuk et al. 2021) Dataset: BRCA1 functional truth set: 1641 missense variants classed deleterious or tolerated by HAP1 cell survival after saturation genome editing	1.4 benignity-likelihood-ratio unitless · higher Uncertainty: Sources conflict: Printed interval (1.14-1.71) has the same log-scale width as this row's positive likelihood ratio interval and is not consistent with the Supplementary Table 6 counts; kept in printed_source_cell only. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source PhD-SNPg-p005 on the BRCA1 functional truth set (Cubuk et al. 2021) brca-20261009-protocol-cubuk2021-brca1 Aggregation: Not reported Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes; Cubuk et al. 2021, Supplementary tables 1-13 (41436_2021_1265_MOESM3_ESM.xlsx) · Supplementary Table 9 (sheet 'SupTable9_Likelihood_Ratios'), G21; tool 'PhD-SNPg-p005'; column 'BRCA1_negative_LR'
Configuration: PhD-SNPg-p005 (Cubuk et al. 2021)	Protocol: BRCA1 functional truth set, binary in silico calls (Cubuk et al. 2021) Dataset: BRCA1 functional truth set: 1641 missense variants classed deleterious or tolerated by HAP1 cell survival after saturation genome editing	234 false-negative-count count · lower Uncertainty: Not applicable: Count Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source PhD-SNPg-p005 on the BRCA1 functional truth set (Cubuk et al. 2021) brca-20261009-protocol-cubuk2021-brca1 Aggregation: Not reported Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes; Cubuk et al. 2021, Supplementary tables 1-13 (41436_2021_1265_MOESM3_ESM.xlsx) · Supplementary Table 6 (sheet 'SupTable6_Tool_Counts'), L49; tool 'PhD-SNPg-p005'; column 'BRCA1_FN'
Configuration: PhD-SNPg-p005 (Cubuk et al. 2021)	Protocol: BRCA1 functional truth set, binary in silico calls (Cubuk et al. 2021) Dataset: BRCA1 functional truth set: 1641 missense variants classed deleterious or tolerated by HAP1 cell survival after saturation genome editing	3.21 likelihood-ratio unitless · higher Uncertainty: CI 2.62 to 3.93. Interval level and method not printed. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source PhD-SNPg-p005 on the BRCA1 functional truth set (Cubuk et al. 2021) brca-20261009-protocol-cubuk2021-brca1 Aggregation: Not reported Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes; Cubuk et al. 2021, Supplementary tables 1-13 (41436_2021_1265_MOESM3_ESM.xlsx) · Supplementary Table 9 (sheet 'SupTable9_Likelihood_Ratios'), F21; tool 'PhD-SNPg-p005'; column 'BRCA1_positive_LR'
Configuration: PhD-SNPg-p005 (Cubuk et al. 2021)	Protocol: BRCA2 functional truth set, binary in silico calls (Cubuk et al. 2021) Dataset: BRCA2 functional truth set: 188 missense variants classed deleterious or tolerated by Homology-directed repair	5.81 benignity-likelihood-ratio unitless · higher Uncertainty: Sources conflict: Printed interval (4.71-7.15) has the same log-scale width as this row's positive likelihood ratio interval and is not consistent with the Supplementary Table 6 counts; kept in printed_source_cell only. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source PhD-SNPg-p005 on the BRCA2 functional truth set (Cubuk et al. 2021) brca-20261009-protocol-cubuk2021-brca2 Aggregation: Not reported Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes; Cubuk et al. 2021, Supplementary tables 1-13 (41436_2021_1265_MOESM3_ESM.xlsx) · Supplementary Table 9 (sheet 'SupTable9_Likelihood_Ratios'), I21; tool 'PhD-SNPg-p005'; column 'BRCA2_negative_LR'
Configuration: PhD-SNPg-p005 (Cubuk et al. 2021)	Protocol: BRCA2 functional truth set, binary in silico calls (Cubuk et al. 2021) Dataset: BRCA2 functional truth set: 188 missense variants classed deleterious or tolerated by Homology-directed repair	6 false-negative-count count · lower Uncertainty: Not applicable: Count Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source PhD-SNPg-p005 on the BRCA2 functional truth set (Cubuk et al. 2021) brca-20261009-protocol-cubuk2021-brca2 Aggregation: Not reported Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes; Cubuk et al. 2021, Supplementary tables 1-13 (41436_2021_1265_MOESM3_ESM.xlsx) · Supplementary Table 6 (sheet 'SupTable6_Tool_Counts'), U49; tool 'PhD-SNPg-p005'; column 'BRCA2_FN'
Configuration: PhD-SNPg-p005 (Cubuk et al. 2021)	Protocol: BRCA2 functional truth set, binary in silico calls (Cubuk et al. 2021) Dataset: BRCA2 functional truth set: 188 missense variants classed deleterious or tolerated by Homology-directed repair	1.99 likelihood-ratio unitless · higher Uncertainty: CI 1.61 to 2.45. Interval level and method not printed. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source PhD-SNPg-p005 on the BRCA2 functional truth set (Cubuk et al. 2021) brca-20261009-protocol-cubuk2021-brca2 Aggregation: Not reported Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes; Cubuk et al. 2021, Supplementary tables 1-13 (41436_2021_1265_MOESM3_ESM.xlsx) · Supplementary Table 9 (sheet 'SupTable9_Likelihood_Ratios'), H21; tool 'PhD-SNPg-p005'; column 'BRCA2_positive_LR'

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Sources and history

Release 2026-10-10-84341e0b121f · Record review: source checked

2 source records and release history

Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes · Original source · Genetics in Medicine 23(11):2096, published 2021-07-06; PMC8553612 full-text XML
Cubuk et al. 2021, Supplementary tables 1-13 (41436_2021_1265_MOESM3_ESM.xlsx) · Original source · 41436_2021_1265_MOESM3_ESM.xlsx

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Technical metadata and extraction receipts

Stable ID: brca-20261009-config-cubuk2021-phd-snpg-p005

areas: dna-genomes
contexts: clinical_research
method types: supervised_machine_learning
reported name: PhD-SNPg-p005
foundation model eligible: false
protocol: Discretisation: TOL (<0.5); DEL (>=0.5)
source locator: Supplementary Table 5 row 49 ('PhD-SNPg', 'PhD-SNPg_p005')
missing metadata: version: reason: unreported; note: Score source: PhD-SNPg webserver (http://snps.biofold.org/phd-snpg/)

Related records

configuration of: PhD-SNPg
system: PhD-SNPg-p005 on the BRCA1 functional truth set (Cubuk et al. 2021)
system: PhD-SNPg-p005 on the BRCA2 functional truth set (Cubuk et al. 2021)

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