Answer:
D. Your daughter's new classmate has Turner syndrome.
Explanation:
Turner syndrome like all diseases require diagnosis by medical experts. People with turner syndrome often exhibit symptoms which are consistent with the descriptions of the middle-school aged daughter. First of all, only females suffer from turner syndrome. They tend to be quite short like she described. They tend to suffer from learning disabilities which might explain  her limited understanding of geometry. They also suffer from broad shoulders  and a webbed neck.
It is believed to be caused by missing X chromosomes. Given the right medical support, girls with the Turner Syndrome can lead productive lives.