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Background  Usher syndrome (USH) is the most common cause of inherited deaf-blindness. The current study aimed to identify pathogenic variants in a Chinese patient with hearing loss and to report the identification of a novel p.(Phe1583Leufs*10) variant in  USH2A,  which met the needs of prenatal diagnosis of the patient's mother .Case presentation  Genomic DNA obtained from a five-year-old girl with hearing loss was analyzed via the hearing loss-targeted gene panels. We identified the compound heterozygous variants c.8559-2A>G and c.4749delT in Usher syndrome type 2A ( USH2A ) gene as the underlying cause of the patient; the former variation has been reported in the literature, but not the latter. The parents of the girl were heterozygous carriers. The two variants were classified as pathogenic. Based on these findings, amniotic fluid samples were used for prenatal diagnosis of the couple's fetus, which was found to carry c.4749delT but not c.8559-2A>G variation. During the follow-up period of more than 9 months after the birth of the fetus, it was confirmed that the infant was healthy.    Conclusions  The results of the present study identified two compound heterozygous  USH2A  variants in a patient with hearing loss and reported a novel  USH2A  variant which expands the spectrum of  USH2A  variants in USH.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12920-021-01052-4.

A novel USH2A variant in a patient with hearing loss and prenatal diagnosis of a familial fetus: a case report