Confidence Intervals for Thresholds of Minor Allele Frequency
This edition of CI 1-α has been specifically designed with the ACMG criteria pertaining to allele frequencies in mind (i.e. PM2, BA1, BS1). These criteria ask a one-sided question. For example, PM2 asks: 'is the population frequency of the variant below a certain threshold value?' or BA1 asks 'is the population frequency of the variant above a certain threshold?'. The allele frequencies in ExAC or gnomAD are based on a sample of the population; hence just because the observed frequency meets the criteria does not necessarily mean the true allele frequency does. A confidence interval is a very useful indicator of how confident we can be that the true allele frequency meets the criteria. Because of the one-sided nature of any pre-specified threshold-based criterion, a one-sided confidence interval is most appropriate. This calculator uses the exact binomial method by default. The exact Poisson method can also be selected.
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