Table 2:
Prevelance of BRCA2 VUS Identified in Malaysia and Singapore
| Variant | No. of carriers (Case) | No. of carriers (Control) | 1000g_EAS_AF | 1000g_EUR_AF | gnomAD_AF_Overall | gnomAD_ EAS_AF | gnomAD_ SAS_AF | gnomAD_ NFE_AF | sub-pop/general pop | Crude odds ratio | p-value |
|---|---|---|---|---|---|---|---|---|---|---|---|
| c.1600G>A (E534K) | 2 | 1 | 1.00E-03 | NA | 2.05E-05 | 2.92E-04 | NA | NA | 14.23 (EAS) | 2.02 | 0.57 |
| c.3782C>G (S1261C) | 1 | 1 | NA | NA | NA | NA | NA | NA | NA | 1.01 | 0.99 |
| c.6322C>T (R2108C) | 119 | 120 | 3.00E-03 | 2.00E-03 | 5.93E-04 | 6.47E-03 | 6.83E-05 | 2.09E-04 | 10.91 (EAS) | 1.00 | 0.98 |
| c.6929C>A (T2310N) | 4 | 4 | NA | NA | 3.26E-05 | NA | 1.96E-04 | NA | 6.02 (SAS) | 1.01 | 0.99 |
| c.8356G>A (A2786T) | 10 | 11 | NA | NA | 6.09e-05 | 8.12E-04 | 3.27E-05 | NA | 13.32 (EAS) | 0.99 | 0.85 |
| c.8393C>T (P2798L) | 1 | 0 | NA | NA | NA | NA | NA | NA | NA | 3.03 | 0.50 |
| c.9104A>G (Y3035C) | 5 | 4 | NA | NA | 2.05E-05 | 2.34E-04 | NA | 9.07E-06 | 11.43 (EAS) | 1.26 | 0.73 |
| c.9104A>T (Y3035F) | 0 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| c.9104A>C (Y3035S) | 0 | 0 | NA | NA | 4.99E-05 | NA | NA | 1.02E-04 | 2.04 (NFE) | NA | NA |
| c.9106C>G (Q3036E) | 4 | 2 | 1.00E-03 | 0 | 3.93E-05 | 5.27E-04 | NA | NA | 13.43 (EAS) | 2.02 | 0.42 |
| c.9344A>G (K3115R) | 1 | 1 | NA | NA | 4.47e-05 | NA | 2.00E-04 | NA | 4.47 (SAS) | 1.01 | 0.99 |
| c.9538C>T (L3180F) | 2 | 2 | 1.00E-03 | NA | 4.06E-05 | 5.22E-04 | NA | NA | 12.85 (EAS) | 1.01 | 0.99 |
| c.9907A>T S3303C) | 1 | 0 | NA | NA | NA | NA | NA | NA | NA | 3.03 | 0.50 |
| c.68–7T>A (IVS2–7T>A) | 5 | 1 | NA | NA | 2.84E-03 | 2.02E-04 | 1.90E-03 | 2.46E-03 | NA* | 5.06 | 0.14 |
| c.632–10dupT (IVS710insT) | 1 | 0 | NA | NA | NA | NA | NA | NA | NA | 3.03 | 0.50 |
| c.8954-5_89542delAACA (IVS225delAACA) | 24 | 26 | NA | NA | 1.06E-04 | 1.51E-03 | NA | NA | 14.14 (EAS) | 0.93 | 0.81 |
1000g_EAS and 1000g_EUR: Allelic frequency in East Asians and Europeans respectively in 1000 genome database; gnomAD_Overall, gnomAD_EAS, gnomAD_SAS, and gnomAD_NFE: Allelic frequency overall, and in East Asians, South Asians and Non-Finnish Europeans respectively in the gnomAD database; Enrichment in Asians: enrichment of variant in either East Asian (EAS) or South Asian (SAS) population compared to the allelic frequency in gnomAD overall
*
indicates MAF»0.3% in general population; Crude odds ratio were calculated using total breast cases (n=7840) vs controls (n=7928); NA: not applicable.