Those are birth defects though. For instance, we still understand humans as being bipedal despite anomalies that prevent a tiny fraction of humans from being bipedal.
Chromosomal abnormalities would be the modern term, it applies to both sexual as well as other chromosomal abnormalities like Down.
But to answer the question as asked: Yes, it fulfills the definition of the older term.
> Is it a birth defect?
Yes.