Abstract
Variants of uncertain significance (VUS) are often challenging for genetic counseling and require additional data for accurate variant classification. This study aims to describe the genotype-phenotype correlation of the seven β-globin gene variants found in Thailand. Retrospective data in a total of 45,914 subjects encountered at our diagnostic laboratory from January 2012 to December 2024 were reviewed. A total of 33 leftover EDTA blood specimens, suspected of having β-globin gene defects, were included. Eighty-nine normal subjects were also analyzed to confirm phenotypic expression of the variants. The whole β-globin and Krüppel-like factor 1 (KLF1) genes were examined using PCR-based methods. Seven nucleotide variants were identified among 33 suspected subjects, including a novel (β(-206(C>G))), four hitherto undescribed in Thailand [β(-198(A>G)), β(IVSII-180(T>C)), β(IVSII-337(A>G)), and β(*233(G>C))], and two known variants [β(-50(G>A)) and β(IVSII-258(G>A))]. The β(-198(A>G)) and β(*233(G>C)) variants were also identified in 1.69% of normal subjects, indicating neutral DNA polymorphisms. All subjects of β(-198(A>G)), β(IVSII-180(T>C)), β(IVSII-258(G>A)), and β(IVSII-337(A>G)) with borderline Hb A(2) levels had KLF1 mutations. Compound heterozygous β(-206(C>G)) and known β(+)-thalassemia trait revealed β-thalassemia trait phenotype. In silico pathogenicity prediction showed that the β(-206(C>G)), β(-198(A>G)), β(IVSII-180(T>C)), β(IVSII-258(G>A)), β(IVSII-337(A>G)), and β(*233(G>C)) were associated with benign variants. It was found that heterozygous β(-50(G>A)) had elevated Hb A(2) levels resembling those of β-thalassemia trait. However, the association of the β(-50(G>A)) and Hb E or β-thalassemia revealed a phenotype of Hb E or β-thalassemia trait. Most prediction tools indicate that the β(-50(G>A)) is associated with benign variants; however, PromoterAI revealed that the β(-50(G>A)) is associated with under-expression of the β-globin gene with high sensitivity. Based on these findings, the β(-50(G>A)) is most likely a very mild β(+)-thalassemia allele. This study described the genotype-phenotype correlation of known and novel β-globin gene variants found in Thailand. The data should prove useful for accurate variant classification, genetic counseling, and a prevention and control program of severe thalassemia diseases in Thailand.