Table 1 Single-nucleotide variation (SNV) characteristics in whole-genome sequences from Estonian Biobank participants

From: Genetic variation in the Estonian population: pharmacogenomics study of adverse drug effects using electronic health records

(a) Variants in the Estonian Biobank discovery set

Whole genome

ADMET genes (n = 64)

 

n

%

n

%

Genes with variants

18,468

 

56

 

Unique variants

29,108,287

 

1314

 

Variant carriers

2240

 

2240

 

Novel variants

11,508,281

39.5

267

20.3

Known variants

17,600,006

60.5

1047

79.7

MAF > 5%

5,403,215

18.6

164

12.5

1% ≤ MAF < 5%

2,444,670

8.4

95

7.2

0.5% ≤ MAF < 1 %

1,211,084

4.2

45

3.4

0.05% ≤ MAF < 0.5%

6,460,248

22.2

285

21.7

MAF < 0.05 %

13,589,070

46.7

725

55.2

AC = 1

10,617,607

36.5

560

42.6

AC = 2

2,971,463

10.2

165

12.6

(b)

Loss-of-function

Missense

Promoter region

 

n

%

n

%

n

%

Unique variants

41

 

567

 

706

 

MAF > 5%

1

2.4

39

6.8

124

17.6

1% < MAF < 5%

0

0

38

6.7

57

8.1

0.5% < = MAF < 1 %

1

2.4

16

2.8

28

3.9

0.05% < = MAF < 0.5%

15

36.6

113

19.9

157

22.2

MAF < 0.05 %

24

58.5

361

63.6

340

48.1

AC = 1

21

51.2

279

49.2

260

36.8

AC = 2

3

7.3

82

14.5

80

11.3

Novel variants

10

24.3

134

23.6

123

17.4

Novel variants AC = 1

6

14.6

99

17.5

50

7.1

Known variants

31

75.6

433

76.4

583

82.5

Known variants AC = 1

15

36.6

180

31.7

210

29.7

  1. AC allele count, MAF Minor allele frequency, ADMET absorption, distribution, metabolism, excretion, and toxicity, n number of variants
  2. (a) Numbers and frequencies of detected variants in whole-genome sequences and targeted pharmacogenes
  3. (b) Characterization of targeted pharmacogenetic variations in loss of function (LoF), missense, and regulatory (transcription factor binding sites in liver 5-kb upstream of gene start site) regions
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