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Table 3 Classification criteria for variants by impact and minor allele frequency

From: Investigating the characteristics of genes and variants associated with self-reported hearing difficulty in older adults in the UK Biobank

  Consequence Pathogenicity Minor allele frequency Number of variants
Meaning The effect of the mutation on the protein How likely the mutation is to impair protein function How rare the alternative allele is in the population  
Source Ensembl, ReMM CADD, Sutr, SpliceAI gnomAD, 1000G, TOPMed, ESP6500  
High impact 5′ UTR variants, splice site mutation, stop gain or loss, start loss, insertion, deletion, duplication, missense variants and variants in mature miRNAs CADD > 25 or Sutr > 1 (for 5′ UTR variants only) or SpliceAI score > 0.5 (for splice site variants only) <0.005 1,141,302
<0.01 1,151,111
<0.05 1,160,767
<0.1 1,162,399
<0.2 1,163,464
<1 1,165,167
Low impact All consequences except for intergenic and intronic variants, variants in transcripts subject to nonsense-mediated decay, and variants up- or downstream of a gene; all variants with a ReMM score > 0.95 Not assessed <0.1 6,398,787