Are congenital abnormalities genetic?

Sometimes. Although it's true that most congenital anomalies (duodenal atresia, ventricular septal defect) have some (currently known or unknown) genetic underpinning, some clearly do not (amniotic band deformation sequence, hydranencephaly, gastroschisis, porencephaly) and some are due to teratogenic exposures unrelated to genetic information (valproic acid, paroxetine, coumadin, (warfarin) enalapril, alcohol).