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Table 5 In silico predictions obtained for variants of unknown significance in the South African cohort

From: BRCA1, BRCA2 and PALB2 mutations and CHEK2 c.1100delC in different South African ethnic groups diagnosed with premenopausal and/or triple negative breast cancer

      In silico prediction programs  
Ethnicity Variant Gene Amino acid change Occurrence Classification Align GVGDa SIFT Mutation Taster PolyPhen Refs
Black c.1843_1845delTCT BRCA1 p.Ser615del 1 3 - - - - [5860]
Black c.4798_4800delAAT BRCA2 p.Asn1600del 1 3 - - - - [61]
Black c.7712A > G BRCA2 p.Glu2571Gly 1 3 C0 Deleterious Disease causing Probably damaging [62]
Black c.9875C > T BRCA2 p.Pro3292Leu 2 3 C0 Affect protein function Disease causing Probably damaging [63]
Black c.118A > G PALB2 p.Arg40Gly 1 3 C0 Affect protein function Polymorphism Probably damaging Novel
Black c.2845 T > C PALB2 p.Cys949Arg 1 3 C0 Affect protein function Disease causing Probably damaging Novel
  1. aSpectrum of prediction classes (C0, C15, C25, C35, C45, C55, C65) with C0 less likely to be deleterious and C65 most likely