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Initial development trends toward "female" characteristics. If an embryo has XY chromosomes then normally a gene on the Y chromosome will start to express which pivots development toward "male" characteristics.

If there's a mutation on the responsible part of the Y chromosome then that expression may not happen stunting the development of "male" characteristics.

Certain disorders can prevent the development of sex organs entirely which can lead to the testes failing to develop and subsequent hormone releases to not happen stunting the development of "male" characteristics.

Other disorders can result in the initial sex organ development, but prevent adequate hormone production which stunts the development of "male" characteristics.

Since "male" characteristics occur later in the development cycle (and not always when they're otherwise "supposed" to) at the point of conception all zygotes are of "the sex that produced the large reproductive cell" and since the current administration views zygotes as fully developed people the current administration accidentally classified all humans as female.

Incidentally there being multiple methods by which one's sex can be determined incongruously from the typical indication of one's chromosomes is just one reason why anti-trans bigotry is stupid.