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Table 3 BRCA2 variants detected in Malaysian carriers by genotyping

From: Characterization of BRCA1 and BRCA2 variants in multi-ethnic Asian cohort from a Malaysian case-control study

HGVS cDNA

HGVS protein

Reported in BICa

AGVGDb

PolyPhen-2c

SIFTd

MAFe (%)

VFf in controls (%)

Breast cancer cases

Healthy controls

ORg

95% CI

p-value

c.215A > G

p.Asn72Ser

1

C0

Benign

Tolerated

0.07

0.21

1/1215

3/1454

0.41

0.04–3.98

0.441

c.440A > G

p.Gln147Arg

16

C0

Benign

Tolerated

0.39

0.62

12/1218

9/1463

1.38

0.58–3.33

0.469

c.943 T > A

p.Cys315Ser

15

C0

Benign

Tolerated

0.50

1.20

18/2055

17/1420

0.79

0.41–1.55

0.496

c.1825C > G

p.Gln609Glu

1

C0

Benign

Damaging

0.06

0.07

2/1218

1/1464

1.65

0.15–18.37

0.683

c.2186 T > C

p.Ile729Thr

0

C0

Benign

Tolerated

0.09

0.28

1/1213

4/1423

0.31

0.04–2.80

0.298

c.3445A > G

p.Met1149Val

8

C0

Benign

Tolerated

0.26

0.48

7/1215

7/1454

0.83

0.29–2.43

0.740

c.4376A > G

p.Asn1459Ser

1

C0

Benign

Tolerated

0.10

0.14

5/2087

2/1462

1.89

0.37–9.80

0.448

c.4779A > C

p.Glu1593Asp

3

C0

Benign

Tolerated

0.14

0.27

6/2088

4/1464

1.15

0.32–4.13

0.834

c.5167A > C

p.Thr1723Pro

1

C0

Possibly damaging

Tolerated

0.04

0.07

1/1214

1/1454

1.05

0.06–16.99

0.976

c.5312G > A

p.Gly1771Asp

44

C0

Benign

Tolerated

0.03

0.07

1/2054

1/1459

0.58

0.04–9.74

0.706

c.5785A > G

p.Ile1929Val

32

C0

Benign

Tolerated

0.82

1.62

20/1213

23/1421

1.03

0.56–1.90

0.916

c.5986G > A

p.Ala1996Thr

4

C55

Probably damaging

Tolerated

0.16

0.34

6/2060

5/1462

0.95

0.29–3.16

0.932

c.6322C > T

p.Arg2108Cys

22

C0

Benign

Tolerated

0.55

1.12

13/1207

16/1431

0.94

0.45–1.98

0.871

c.6325G > A

p.Val2109Ile

8

C0

Benign

Tolerated

0.25

0.49

6/1213

7/1422

0.89

0.30–2.69

0.837

c.7052C > G

p.Ala2351Gly

6

C0

Possibly damaging

Damaging

0.21

0.49

8/2077

7/1422

0.78

0.28–2.17

0.627

c.7469 T > C

p.Ile2490Thr

240

C0

Benign

Tolerated

0.06

0.07

3/2060

1/1462

2.27

0.24–21.90

0.480

c.8187G > T

p.Lys2729Asn

24

C0

Probably damaging

Damaging

0.63

1.30

15/1218

19/1463

0.98

0.50–1.95

0.964

c.8356G > A

p.Ala2786Thr

2

C0

Probably damaging

Damaging

0.17

0.28

8/2088

4/1448

1.52

0.45–5.07

0.498

c.8702G > A

p.Gly2901Asp

3

C65

Probably damaging

Damaging

0.11

0.34

1/1217

5/1464

0.25

0.03–2.16

0.208

c.9104A > G

p.Tyr3035Cys

3

C55

Probably damaging

Damaging

0.06

0.07

2/1213

1/1454

2.34

0.21–26.02

0.489

c.9538C > T

p.Leu3180Phe

1

C0

Probably damaging

Damaging

0.04

0.14

1/2089

2/1448

0.34

0.03–3.81

0.382

c.10234A > G

p.Ile3412Val

114

C0

Benign

Tolerated

1.42

2.53

40/1217

37/1464

1.29

0.81–2.04

0.280

c.68-7 T > A

-

3

Not applicableh

0.07

0.07

4/2076

1/1458

3.10

0.34–28.31

0.316

c.516 + 18 T > C

-

1

Not applicableh

0.29

0.49

8/1207

7/1417

1.41

0.51–3.91

0.511

c.8954-5_8954-2delAACA

-

0

Not applicableh

0.06

0.14

2/2088

2/1463

0.83

0.12–5.93

0.855

  1. a Breast Cancer Information Core (http://research.nhgri.nih.gov/bic/), an open access online breast cancer mutation database assessed by Oct 2015
  2. b AGVGD grades: C0, C15, C25, C35, C45, C55, C65 with C65 most likely to interfere with function and C0 least likely. The probability was assessed using the alignment of which from human to sea urchin in BRCA2
  3. c PolyPhen-2 grades: Benign, Possibly damaging, Probably damaging
  4. d SIFT grades: Tolerated, Damaging
  5. e Minor allele frequency, which was detected in the entire cohort
  6. f Variant frequency, which was detected only in healthy controls
  7. g Odds ratio, adjusted for ethnicity, age and family history using logistic regression
  8. h AGVGD, PolyPhen-2 and SIFT analyses can only predict the effect of missense variant