Centronuclear myopathy (CNM) is one of the congenital myopathies characterized by centrally located nuclei in the muscle fibers. Currently, more than 30 pathogenic variants in the dynamin 2 (DNM2) genes have been identified. Here, we describe a 63-year-old female who presented with slowly progressive limb weakness with no facial weakness or ophthalmoplegia. Electromyographical myotonia without clinical myotonia was noted. In the DNM2 gene, whole-genome sequencing revealed the heterozygous variant c.1936G>T (p.Asp646Tyr), which was not reported previously. Muscle pathology identified many fibers with centrally located nuclei, with the predominance of type 1 fibers. Thus, the patient was finally diagnosed with DNM2-associated CNM with a novel pathogenic variant and with unusually mild phenotype.