Table 3.

Likely Benign Variants in PTEN Exon 5 Identified in the Study Population

Patients	Nucleotide change	Amino acid change	Variation type	ID rs	Genotype	REVEL score	Clinvar prediction	Reported in	Frequency in breast cancer in other studies
3. 8 .10 .45	c.319G>A	D107N	Missense	rs57374291	Heterozygous	0.581	-	dbSNP	32/350 patients, Pakistan (Baig et al., 2011), 1/72patients, Iran (Nassiri et al., 2009)
45. 69	c.343G>A	D115N	Missense	rs145124907	Heterozygous	0.390	-	dbSNP	10/350 patients, Pakistan (Baig et al., 2011)
11 . 54. 60	c.457G>A	D153N	Missense	rs9651492	Heterozygous	0.501	Uncertain significance	Clinvar, dbSNP, ClinGen	33/350 patients, Pakistan (Baig et al., 2011), 1/43 patients, Greece (Kechagioglou et al., 2014), 2/51 patients, Egypt (Elwy et al., 2023)
14. 15. 28	c.462C>A	F154L	Missense	-	Heterozygous	0.585	-	-
17. 45. 53. 60. 67	c.462C>G	F154L	Missense	-	Heterozygous	0.585	Uncertain significance	dbSNP, Clinvar
3. 11. 47. 52. 54. 57. 60. 65	c.482G>A	R161K	Missense	-	Heterozygous	0.539	-	-	18/350 patients, Pakistan (Baig et al., 2011), 1/50 patients, China (Yang et al., 2010)