Thalassemia is a common hemoglobin disorder caused by genetic defects in a single autosomal gene. Based on the deficient globin strand, it can be classified as α-thalassemia or β-thalassemia. The 27.6 kb deletion on α-globin related gene cluster (-α27.6) is a rare α-thalassemia variant discovered in 2011, which could affect the detection of common α-thalassemia variants and cause misdiagnosis. An α-thalassemia variant carrying a Chinese couple was reported in this study. The wife was diagnosed at another hospital as αCSα/αCSα but did not manifest corresponding symptoms. After further examinations and in-depth analyses of the results, the genotype of the wife was finally confirmed to be -α27.6/αCSα. Meanwhile, the genotype of the husband was diagnosed as αCSα/αα. The couple requested prenatal diagnosis in the worry of α-thalassemia caused by αCSα/αCSα. Genetic tests on the amniotic fluid reported a mild thalassemia-related genotype of αCSα/αα, on which our suggestion of continuing pregnancy was based. The -α27.6/αCSα case and related manifestations were first reported here expanding the gene spectrum of thalassemia. Such genotype can be misdiagnosed as αCSα/αCSα causing inaccurate estimations of thalassemia risk. To avoid these misdiagnoses, genetic tests for deletions in the related regions were advised when inconsistencies between the genotype and the phenotype were discovered.