https://static.scientificamerican.com/sciam/assets/File/Pitch_sketch_final.png?w=2000

This is the best resource I've seen to show things relatively simply.

The TL;DR is that a whole "Y" chromosome isn't exactly responsible for "maleness", the SRY gene is. It's normally on the Y chromosome, but mutations can occur placing that gene onto the X chromosome. Inversely, someone could inherit a Y chromosome without that gene, in which case they would develop with female traits.

It's not considered trans because someone with 46XX plus the SRY gene would develop male genitalia, be identified as male at birth, and likely identify themselves as male. For some types of these conditions, there are plenty of people walking around with no clue that their chromosomes don't match their gender.

Disclaimer: I'm not a geneticist, so i could have explained something a little off.

I googled it for you.

https://en.wikipedia.org/wiki/XX_male_syndrome

In 90 percent of these individuals, the syndrome is caused by the Y chromosome's SRY gene, which triggers male reproductive development, being atypically included in the crossing over of genetic information that takes place between the pseudoautosomal regions of the X and Y chromosomes during meiosis in the father.[2][7] When the X with the SRY gene combines with a normal X from the mother during fertilization, the result is an XX genetic male. Less common are SRY-negative individuals, those who are genetically females, which can be caused by a mutation in an autosomal or X chromosomal gene.[2] The masculinization of XX males is variable.

You've heard of xy people and xx people, but wait till you hear about X people!

Or xxx people, or xxy people, or... dies

cis just means your current gender identity is the same that was assigned to you at birth. there are cases where someone has XX chromosomes, but the body develops as male.

Maybe she means the exceptions?

Exceptions: While XX and XY are the most common sex chromosome combinations, there are exceptions, such as individuals with variations in their sex chromosomes, such as XXY (Klinefelter syndrome) or XYY.