Stargardt disease (STGD1) is an inherited retinal dystrophy that follows an autosomal recessive inheritance in which photoreceptors degenerate, leading to progressive vision loss that starts from the central retina. The severity of symptoms can vary considerably depending on the mutations: they range from severe childhood-onset to late-onset milder forms, the latter being caused by specific hypomorphic variants. In this study, we describe a novel non-canonical splicing variant: NM_000350.3:c.5461-6T>C. This variant was found in compound heterozygosity with a frequent pathogenic hypomorphic variant, p.Gly1961Glu, in a patient with Stargardt disease and her affected brother. In silico tools predicted a low effect on splicing, but experimental validation, in contrast, showed this DNA change to be causing severe splicing alterations.