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Table 3 Promoter and intronic sequence variations of the NBN gene in French Canadian breast cancer cases and healthy controls.

From: Variations in the NBN/NBS1 gene and the risk of breast cancer in non-BRCA1/2French Canadian families with high risk of breast cancer

SNP

SNP ID1

(dbSNP ID)

Location

Series (No.)

MAF2

Common homozygote No. (expected)3

Heterozygote No. (expected)3

Rare homozygote No. (expected)3

HWE p-value

OR (95% CI)4

Reported MAF in Caucasian

10

c.-110-242delAGTA

Promoter

Cases (97)

0.082

81 (81.66)

16 (14.68)

0 (0.66)

0.38

3.4

 
 

(rs36226237)

 

Controls (72)

0.028

68 (68.06)

4 (3.89)

0 (0.06)

0.81

(1.1–10.5)

 

11

c.702+149T/C

Intron 6

Cases (97)

0.082

83 (81.66)

12 (14.68)

2 (0.66)

0.07

0.7

0.108–0.1175

 

(rs3026271)

 

Controls (73)

0.089

60 (60.58)

13 (11.84)

0 (0.58)

0.40

(0.3–1.6)

 

12

c.703-29C/T

Intron 6

Cases (97)

0.015

94 (94.02)

3 (2.95)

0 (0.02)

0.88

1.1

0.0215

 

(NA)6

 

Controls (73)

0.014

71 (71.01)

2 (1.97)

0 (0.01)

0.91

(0.2–7.0)

 

13

c.703-18G/A

Intron 6

Cases (97)

0.026

92 (92.06)

5 (4.87)

0 (0.06)

0.79

3.9

 
 

(rs769418)

 

Controls (73)

0.007

72 (72.00)

1 (0.99)

0 (0)

0.95

(0.4–34.2)

 

14

c.896+36G/A

Intron 7

Cases (97)

0.026

92 (92.06)

5 (4.87)

0 (0.06)

0.79

3.9

0.021–0.055

 

(rs1805826)

 

Controls (73)

0.007

72 (72.00)

1 (0.99)

0 (0)

0.95

(0.4–34.2)

 

15

c.897-42G/C

Intron 7

Cases (97)

0.015

94 (94.02)

3 (2.95)

0 (0.02)

0.76

0.4

 
 

(NA)6

 

Controls (73)

0.034

68 (68.09)

5 (4.83)

0 (0.09)

0.76

(0.1–1.9)

 

16

c.994+233G/A

Intron 8

Cases (97)

0.294

50 (48.37)

37 (40.25)

10 (8.37)

0.43

0.7

0.285

 

(rs6990969)

 

Controls (74)

0.311

34 (35.15)

34 (31.70)

6 (7.15)

0.53

(0.4–1.4)

 

17

c.1124+18C/T

Intron 9

Cases (97)

0.278

52 (50.52)

36 (38.97)

9 (7.52)

0.45

0.7

0.09–0.3065

 

(rs2234744)

 

Controls (74)

0.304

35 (35.84)

33 (31.32)

6 (6.84)

0.64

(0.4–1.4)

 

18

c.1124+91C/A

Intron 9

Cases (97)

0.273

53 (51.24)

35 (38.52)

9 (7.24)

0.37

0.7

0.283–0.3065

 

(rs1805818)

 

Controls (74)

0.304

35 (35.84)

33 (31.32)

6 (6.84)

0.64

(0.4–1.3)

 

19

c.1125-79C/A

Intron 9

Cases (97)

0.284

52 (49.80)

35 (39.41)

10 (7.80)

0.27

0.8

0.3235

 

(rs1805786)

 

Controls (72)

0.292

36 (36.13)

30 (29.75)

6 (6.13)

0.94

(0.4–1.5)

 

20

c.1915-7A/G

Intron 12

Cases (97)

0.284

52 (49.80)

35 (39.41)

10 (7.80)

0.27

0.8

0.20–0.3125

 

(rs2308962)

 

Controls (70)

0.300

34 (34.30)

30 (29.40)

6 (6.30)

0.86

(0.4–1.5)

 

21

c.2071-30A/T

Intron 13

Cases (97)

0.284

52 (49.80)

35 (39.41)

10 (7.80)

0.27

0.7

 
 

(rs3736639)

 

Controls (71)

0.310

33 (33.82)

32 (30.37)

6 (6.82)

0.65

(0.4–1.3)

 

22

c.2234+86T/G

Intron 15

Cases (97)

0.010

95 (95.01)

2 (1.98)

0 (0.01)

0.92

3.8

 
 

(NA)

 

Controls (72)

0.000

72 (72.00)

0 (0)

0 (0)

1.00

(0.2–80.3)

 

23

c.2234+88C/G

Intron 15

Cases (97)

0.015

94 (94.02)

3 (2.95)

0 (0.02)

0.88

0.4

0.017–0.0425

 

(rs13312970)

 

Controls (71)

0.035

66 (66.09)

5 (4.82)

0 (0.09)

0.76

(0.1–1.8)

 

24

c.2234+157A/G

Intron 15

Cases (97)

0.046

88 (88.21)

9 (8.58)

0 (0.21)

0.63

2.3

0.000–0.0255

 

(rs13312971)

 

Controls (71)

0.021

68 (68.03)

3 (2.94)

0 (0.03)

0.86

(0.6–8.9)

 
  1. 1 According to the nomenclature guidelines of the Human Genome Variation Society (reference sequence NM_002485.4), nucleotide number one being the A from the ATG codon. 2 Minor allele frequency 3 As expected under Hardy-Weinberg equilibrium 4 Odds ratios for comparison of heterozygotes versus common homozygotes 5 From NCBI dbSNP data. 6 No entry in NCBI dbSNP database, although reported in the literature.
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