Fig. 3

Number of publications for variants observed at an allele frequency greater than 0.01%. a The top box plot, in blue, summarizes the publication of a randomly selected set of 100 variants with a consensus classification of benign in ClinVar and having an allele frequency greater than 0.01%. The bottom box plot, in red, summarizes the publication counts of all 129 variants with a consensus classification of pathogenic in ClinVar and having an allele frequency greater than 0.01%. The box represents the 25th–75th percentile range, with the median publication count depicted as the horizontal line in the middle. The “whiskers” represents the maximum and minimum values. b Scatter plot of allele frequencies and publication counts of the same set of variants. Each red circle represents a pathogenic variant and each blue circle represents a benign variant. x-axis: allele frequency; y-axis: publication counts. Four pathogenic variants that are extreme outliers were excluded for display purposes: (1) GJB2 NM_004004.5:c.35delG (p.Gly12Valfs*2) has an allele frequency of 0.60% and reported in 496 publications; (2) CFTR NM_000492.3:c.1521_1523delCTT (p.Phe508del) has an allele frequency of 0.68% and reported in 966 publications; (3) SERPINA1 NM_001127701.1:c.1096G > A (p.Glu366Lys) has an allele frequency of 1.2% and reported in 56 publications; and (4) BTD NM_000060.3:c.1330G > C (p.Asp444His) has an allele frequency of 3.2% and reported in 46 publications