Table 3.

Classification of variants in BRCA2

BRCA2 unclassified variantOccurrence in 180 ABCFS controlsFrequency in Myriad database (with a deleterious mutation)Bayes factor (no. families)Co-occurrenceSequence conservationA-GVGDLOH (no. tumors)Histopathology (no. tumors)Odds of causality, genetic data (frequency with a deleterious mutation and segregation data)Odds of causality, sequence data (sequence conservation and A-GVGD)Odds of causality, pathology dataOdds of causality, without pathology data (LOH and immunohistopathology)Combined odds of causality (genetic, sequence, and pathology data)Model classification
353 A > G (Y42C)1255 (11)0.023 (2)<0.00010.190Not valid0.08180, no LOH (2)1.440 (2)<0.000011.0000.11779<0.00001<0.00000Neutral
1379 C > T (S384F)0182 (4)0.0987 (1)0.21040.008Not valid0.06700, loss of UV (1)1.000 (NA)0.020771.0000.067000.020770.00139Neutral
2834 C > T (S869L)01 (0)9.43 (1)1.15600.005Valid, EN0.01916, no LOH (1), loss of UV (1)0.520 (1)10.901080.0050.009960.054510.00054Neutral
4021 T > A (C1265S)000.042 (1)1.02940.008Valid, EN0.28600, no LOH (1)1.000 (NA)0.043230.0080.286000.000350.00010Neutral
7049 G > T (G2274V)019 (0)0.215 (1)2.24900.008Valid, EN0.01916, loss of UV (1), no LOH (1)1.200 (1)0.483540.0080.022990.003870.00009Neutral
7181 G > A (R2318Q)05 (0)0.1264 (2)1.02945.000Valid, ED0.01916, no LOH (1), loss of UV (1)1.000 (NA)0.130125.0000.019160.650580.01247NA
8204 G > C (R2659T)01 (0)14.7 (1)1.00005.000Valid, ED0.28600, no LOH (2)1.200 (1)14.700005.0000.3432073.5000025.22520NA
8216 A > T (E2663V)09 (0)1.0 (1)1.22505.000Valid, ED0.06700, loss of UV (1)0.520 (1)1.225005.0000.034846.125000.21340NA
8222 A > G (D2665G)129 (1)0.0021 (1)1.73305.000Valid,ED0.06700, loss of UV (1)1.200 (1)0.003645.0000.080400.018200.00146Neutral
8237 C > T (S2670L)08 (1)2.0 (1)1.22500.190Not valid0.06700, loss of UV (1), no LOH (1)1.000 (NA)2.450001.0000.067002.450000.16415NA
8395 G > C (D2723H)042 (0)7.4 (2)3.37205.000Valid, ED5.27000, loss of WT (1)0.624 (2)24.952805.0003.28848124.76400410.28392NA
8536 G > A (A2770T)000.41 (1)1.00005.000Valid, ED1.00000 (NA)1.200 (1)0.410005.0001.200002.050002.46000NA
8714 A > G (del exon 19)0039.20 (1)1.00005.000Valid, ED0.28600, no LOH (1)0.520 (1)39.200005.0000.14872196.029.14912NA
8795 A > C (E2856A)1239 (3)1.05 (2)1.06400.190Valid, EN0.00449, loss of UV (2)1.200 (1)1.117200.1900.005390.212270.00114Neutral
  • Abbreviations: UV, unclassified variant; WT, wild type; NA, not applicable; EN, enriched neutral; ED, enriched deleterious.