Congenital refers to something present at birth but not necessarily inherited from the parents. Babies with heart disorders developed in utero can live long and productive lives, in spite of their congenital birth defect.
Congenital derives from the Latin genus, to beget. Something that is present at one’s begetting, during fetal development, or at birth is congenital. Fetal alcohol syndrome, which develops in fetuses if their mothers are drinking heavily while pregnant, is a congenital disorder. You might also use congenital to describe something seemingly inborn “a congenital sense of humor,” or a “congenital faith.”