Profiling structural variations of the α-globin gene cluster by the single molecule real-time sequencing: remarkable diversity of the spectrum with rare and novel variants identified in a large Chinese cohort

α-thalassemia is an inherited monogenic disorder that exhibits a notably high prevalence in the Guangxi region of China. Subjects in this study were recruited from the Second Affiliated Hospital of Guangxi Medical University between October 2021 and December 2024. Hematological phenotypes were evaluated, followed by structural variations profiling using SMRT sequencing. Novel structural variants were validated using multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing, while hematological phenotypic analysis was performed on the corresponding pedigrees. In this cohort of 1,430 subjects, 381 subjects (26.64%, 381/1430) exhibited structural variations in the α-globin gene cluster. Of the 381 subjects with α-globin structural variants, 355 were heterozygotes, 23 were compound heterozygotes, and 3 were homozygotes, collectively accounting for 407 alleles. SMRT analysis identified fourteen distinct structural variants, with the --SEA deletion representing the predominant variant at a frequency of 60.44% (246/407), followed by the -α3.7 (23.34%, 95/407) and -α4.2 (10.07%, 41/407) deletions. Furthermore, eleven rare variants were detected at an aggregate frequency of 6.14% (25/407), including --THAI, -α2.4, -α21.9, --11.1, HKαα, --120 (chr16:85493–205576 del), --35.2 (chr16:150825–186025 del), αααanti3.7, αααanti4.2, αααα3.7, and (αα)Fusion. Notably, two novel α0-thalassemia deletions (--120 and --35.2) associated with microcytic hypochromic anemia were identified, representing previously unreported rare deletions. The structural variation of the α-globin gene cluster is remarkably diverse. The novel variants identified in this study expand the variant spectrum in thalassemia. These findings provide support for thalassemia genetic counseling, diagnosis, and disease management. SMRT sequencing demonstrates superior capability in variant detection and significant potential for clinical diagnostic applications.