Genotype-Phenotype Correlation of Seven Known and Novel β-Globin Gene Variants

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), βIVSII−180(T>C), βIVSII−337(A>G), and β*233(G>C)], and two known variants [β−50(G>A) and βIVSII−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), βIVSII−180(T>C), βIVSII−258(G>A), and βIVSII−337(A>G) with borderline Hb A2 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), βIVSII−180(T>C), βIVSII−258(G>A), βIVSII−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 A2 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.