Actually, prevalence of transsexual women (the accepted term for what you meant, since "women" is what they identify as) is probably quite a bit higher than that. http://ai.eecs.umich.edu/people/conway/TS/TSprevalence.html does an analysis that concludes that said prevalence is on the order of 1 in 500.
But I don't think we were talking about transsexuality, which is something different from the intersex conditions which might make this whole business of sex testing more complicated than one might expect.
prevalence of Klinefelter's syndrome (XXY male, with symptoms): 1 in 1000 men
prevalence of Transsexual men ("biological" men who identify as women): 1 in 30,000 to 1 in 4,500
(source: Wikipedia, but the references for these statistics appear to be in legitimate scientific publications)