Far more births are true hermaphroditism than most realize. It is rare, but not that rare. How are they listed at birth? In almost all cases a decision must be made between boy and girl. The rule is “If a penis then it is a boy”. It is listed as boy. However, something must be done.
It is far easier and safer to delete the penis and inner scrotum than cutting out the female organs. Almost always it is quickly changed to girl and the birth certificate altered.