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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