Configuration

Polyphen2_HDIV (Cubuk et al. 2021)

Polyphen2 HumDIV scores dichotomised at the cited threshold.

Overview

Polyphen2 HumDIV 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: Polyphen2_HDIV (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	27.6 benignity-likelihood-ratio unitless · higher Uncertainty: Sources conflict: Printed interval (26.9-28.3) 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 Polyphen2_HDIV 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'), G36; tool 'Polyphen2_HDIV'; column 'BRCA1_negative_LR'
Configuration: Polyphen2_HDIV (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	2 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 Polyphen2_HDIV 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'), L53; tool 'Polyphen2_HDIV'; column 'BRCA1_FN'
Configuration: Polyphen2_HDIV (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	1.16 likelihood-ratio unitless · higher Uncertainty: CI 1.14 to 1.19. Interval level and method not printed. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Polyphen2_HDIV 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'), F36; tool 'Polyphen2_HDIV'; column 'BRCA1_positive_LR'
Configuration: Polyphen2_HDIV (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	7.28 benignity-likelihood-ratio unitless · higher Uncertainty: Sources conflict: Printed interval (6.78-7.81) 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 Polyphen2_HDIV 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'), I36; tool 'Polyphen2_HDIV'; column 'BRCA2_negative_LR'
Configuration: Polyphen2_HDIV (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 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 Polyphen2_HDIV 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'), U53; tool 'Polyphen2_HDIV'; column 'BRCA2_FN'
Configuration: Polyphen2_HDIV (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	1.11 likelihood-ratio unitless · higher Uncertainty: CI 1.03 to 1.19. Interval level and method not printed. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Polyphen2_HDIV 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'), H36; tool 'Polyphen2_HDIV'; 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-polyphen2-hdiv

areas: dna-genomes
contexts: clinical_research
method types: supervised_machine_learning
reported name: Polyphen2_HDIV
foundation model eligible: false
protocol: Discretisation: TOL (benign =< 0.452); DEL (probably damaging >=0.957, possibly damaging 0.453 - 0.956)
source locator: Supplementary Table 5 row 54 ('Polyphen2 HumDIV', 'Polyphen2_HumDIV')
missing metadata: version: reason: unreported; note: Score source: Annovar (ljb26_all database)

Related records

configuration of: PolyPhen-2
system: Polyphen2_HDIV on the BRCA1 functional truth set (Cubuk et al. 2021)
system: Polyphen2_HDIV on the BRCA2 functional truth set (Cubuk et al. 2021)

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