Background CAP+1 [A>C] (HBB:c.‐50A>C) is a rare silent β‐thalassemia (β‐thal) mutation. Carrier individuals of this mutation show borderline hemoglobin (Hb), mean corpuscular volume (MCV) and Hb A2 levels. This mutation was previously reported in combination with different β‐thalassemia mutations, leading to variable phenotypes. Case presentation Here, we describe for the first time the combination of silent CAP+1 [A>C] (HBB:c.‐50A>C) mutation with β0 codon 5 [‐CT] (HBB:c.17_18delCT) mutation in a Syrian proband, leading to beta thalassemia intermedia (TI). Conclusions The compound heterozygotes of the silent CAP+1 (A>C) together with another severe beta gene mutation, are phenotypically severe enough to present at an early age and require appropriate therapeutic modalities.