Conotruncal defects (CTD) including tetralogy of Fallot (TOF), double outlet right ventricle (DORV), transposition of great arteries (TGA), and persistent truncus arteriosus (PTA). Conventionally, CTD and thymic hypoplasia occur simultaneously are usually suggestive findings of 22q11.2 deletion syndrome. However, here we describe a fetus with TOF, absence of ductus arteriosus, and thymic hypoplasia diagnosed by echocardiography whose copy number variation sequencing (CNV-Seq) results showed that the fetus had a 17p13.3 microdeletion instead of 22q11.2 deletion syndrome.