Configuration

phastCons100way_vertebrate (Cubuk et al. 2021)

phastCons100way (vertebrate) scores dichotomised at the cited threshold.

Overview

phastCons100way (vertebrate) scores dichotomised at the cited threshold.

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Evaluations and results

2 evaluations · 5 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: phastCons100way_vertebrate (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	5.4 benignity-likelihood-ratio unitless · higher Uncertainty: Sources conflict: Printed interval (5.14-5.66) 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 phastCons100way_vertebrate 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'), G40; tool 'phastCons100way_vertebrate'; column 'BRCA1_negative_LR'
Configuration: phastCons100way_vertebrate (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	24 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 phastCons100way_vertebrate 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'), L46; tool 'phastCons100way_vertebrate'; column 'BRCA1_FN'
Configuration: phastCons100way_vertebrate (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	1.43 likelihood-ratio unitless · higher Uncertainty: CI 1.37 to 1.51. Interval level and method not printed. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source phastCons100way_vertebrate 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'), F40; tool 'phastCons100way_vertebrate'; column 'BRCA1_positive_LR'
Configuration: phastCons100way_vertebrate (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	0 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 phastCons100way_vertebrate 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'), U46; tool 'phastCons100way_vertebrate'; column 'BRCA2_FN'
Configuration: phastCons100way_vertebrate (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	1.3 likelihood-ratio unitless · higher Uncertainty: CI 1.18 to 1.44. Interval level and method not printed. Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source phastCons100way_vertebrate 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'), H40; tool 'phastCons100way_vertebrate'; column 'BRCA2_positive_LR'

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Sources and history

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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-phastcons100way-vertebrate

areas: dna-genomes
contexts: clinical_research
method types: specialist
reported name: phastCons100way_vertebrate
foundation model eligible: false
protocol: Discretisation: TOL (=< 0.99); DEL (> 0.99)
source locator: Supplementary Table 5 row 47 ('phastCons100way (vertebrate)', 'phastCons100way_vertebrate')
version: Scores from Annovar (dbnsfp35c database)

Related records

configuration of: phastCons
system: phastCons100way_vertebrate on the BRCA1 functional truth set (Cubuk et al. 2021)
system: phastCons100way_vertebrate on the BRCA2 functional truth set (Cubuk et al. 2021)

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