BACKGROUND: Copy number variants (CNVs) are an important source of normal and pathogenic genome variations. Especially CNVs identified in prenatal cases need careful considerations and correct interpretation if those are harmless or harmful variants from the norm. The literature on 8q24.22q24.23 microdeletion is rare, which is a challenge for genetic counselling. CASE PRESENTATION: We have performed prenatal diagnosis and genetic counseling of a paternally inherited 8q24.22q24.23 microdeletion. In this family, father with normal phenotype and fetus with abnormal phenotype have the same microdeletion. CONCLUSION: Chromosomal microdeletions and microduplications are difficult to detect by conventional cytogenetics, combination of prenatal ultrasound, karyotype analysis, copy number variation sequencing (CNV-seq), whole-exome sequencing (WES) and genetic counseling is helpful for the prenatal diagnosis of chromosomal microdeletions/microduplications.