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Table 4 Variants in clinical annotation databases observed in healthy cohorts, binned by maximum ethnicity-specific allele frequency across cohorts. Bins are non-cumulative and intervals exclude the value of the upper boundary

From: Integrating 400 million variants from 80,000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts

Source 0 0–0.001 0.001–0.005 0.005–0.01 0.01–0.05 0.05–0.1 0.1–0.5 ≥0.5 Total
ClinVar: pathogenic 30.09 2.59 0.86 0.20 0.26 0.05 0.14 0.02 34.21
ClinVar: likely pathogenic 3.26 0.29 0.08 0.01 0.02     3.66
ClinVar: risk factor 0.35 0.03 0.06 0.02 0.05 0.02 0.13 0.10 0.76
ClinVar: association 0.01 <0.01 <0.01 0.01 0.01 <0.01 0.05 0.02 0.10
ClinVar: likely benign 0.47 0.95 1.01 0.49 0.51 0.05 0.05 0.01 3.54
ClinVar: benign 0.49 0.26 0.47 0.62 2.33 1.10 2.61 1.70 9.58
ClinVar: protective <0.01   <0.01    <0.01 0.02 0.01 0.03
ClinVar: drug response <0.01     <0.01   0.01 0.01 0.02
ClinVar: uncertain significance 8.15 2.05 1.53 0.37 0.36 0.05 0.06 0.03 12.60
ClinVar: other 1.02 0.05 0.04 0.02 0.03 0.01 0.15 0.08 1.40
ClinVar: unknown 29.44 2.58 0.97 0.19 0.38 0.12 0.31 0.11 34.10
HGMD: DM 81.24 4.17 1.40 0.39 0.46 0.05 0.04 0.01 87.76
HGMD: DM? 4.80 0.61 0.50 0.17 0.35 0.12 0.17 0.02 6.74
HGMD: DFP 0.16 0.01 0.02 0.01 0.07 0.08 0.48 0.29 1.12
HGMD: DP 0.30 0.03 0.06 0.04 0.13 0.09 0.71 0.45 1.81
HGMD: FP 0.86 0.15 0.16 0.09 0.20 0.09 0.32 0.15 2.02
HGMD: FTV 0.32 0.06 0.03 0.01 0.03 0.01 0.04 0.03 0.53
OMIM: pathogenic 72.24 8.69 3.19 1.00 1.14 0.26 0.73 0.23 87.48
OMIM: probably pathogenic 0.02         0.02
OMIM: probably not pathogenic    0.01       0.01
OMIM: risk factor 1.33 0.23 0.28 0.06 0.29 0.13 0.59 0.57 3.48
OMIM: association 0.02 0.01   0.01   0.01 0.06 0.09 0.20
OMIM: no known pathogenicity 0.11 0.03 0.04 0.03 0.11 0.06 0.39 0.15 0.92
OMIM: confers sensitivity        0.01   0.01
OMIM: protective 0.01   0.01    0.03 0.06 0.05 0.16
OMIM: drug response   0.01    0.02   0.05 0.07 0.15
OMIM: other 6.46 0.32 0.15 0.06 0.03 0.03 0.04 0.01 7.10
OMIM: VUS 0.11 0.08 0.07 0.03 0.03 0.05 0.09 0.05 0.51
  1. Values represent the percentage of variants from the respective resource that fall into each category and bin. DM, disease-causing mutation; DM?, likely DM; DP, disease-associated polymorphism; DFP, DP with additional functional evidence; FP, functional polymorphism; FTV, frameshift or truncating; VUS, variant of unknown significance