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

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

					In silico prediction programs
Ethnicity	Variant	Gene	Amino acid change	Occurrence	Classification	Align GVGD^a	SIFT	Mutation Taster	PolyPhen	Refs
Black	c.1843_1845delTCT	BRCA1	p.Ser615del	1	3	-	-	-	-	[58–60]
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

^aSpectrum of prediction classes (C0, C15, C25, C35, C45, C55, C65) with C0 less likely to be deleterious and C65 most likely

ISSN: 1471-2407