Method

50 bp rule for nonsense-mediated decay

Labels a stop-gain variant as triggering nonsense-mediated decay when the new stop codon lies more than 50 base pairs upstream of the last exon junction in the coding region; a binary score.

1 evaluation · 1 result

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1 evaluation · 1 result. Different protocols are not a single leaderboard.

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Method: 50 bp rule for nonsense-mediated decay	Protocol: ClinVar stop-gain pathogenicity by NMD status, ROC-AUC (Brandes et al. 2023 Fig. 6d, Supplementary Table 2) Dataset: ClinVar stop-gain variants, pathogenic vs benign (Brandes et al. 2023)	0.662 AUROC (ROC-AUC, pathogenic versus benign ClinVar all stop-gains; zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 50bp rule on all stop-gains (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-stop-gains Aggregation: Not reported Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Supplementary Table 2 sheet 'Table_of_results_stop_gains' cell D5, row '50bp rule', column 'AUC_ALL'

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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

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Genome-wide prediction of disease variant effects with a deep protein language model (Brandes et al., Nature Genetics 2023) · Original source · Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10)

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Technical metadata and extraction receipts

Stable ID: gfm-guides-20261014-esm1b-method-nmd-50bp-rule

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
reported name: 50bp rule
entity level: method
source locator: Methods 'Baseline scores of indel and stop-gain variant effects'
missing metadata: version: reason: inapplicable; note: Baseline defined in the article's Methods

Related records

system: 50bp rule on all stop-gains (Brandes et al. 2023)

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