These statistics are approximations.
Not XX and not XY one in 1,666 births
Klinefelter (XXY) one in 1,000 births
Androgen insensitivity syndrome (male who is resistant to male hormones) / one in 13,000 births
Partial androgen insensitivity syndrome / one in 130,000 births
Classical congenital adrenal hyperplasia (adrenal gland dysfunction) / one in 13,000 births
Late onset adrenal hyperplasia / one in 66 individuals
Vaginal agenesis (the vagina doesn't develop at all, and the womb partially or doesn't develop) / one in 6,000 births
Ovotestes (gonads with male and female traits) / one in 83,000 births
Idiopathic (no discernable medical cause) / one in 110,000 births
Iatrogenic (caused by medical treatment, for instance progestin administered to pregnant mother) / no estimate
5 alpha reductase deficiency / no estimate
Mixed gonadal dysgenesis / no estimate
Complete gonadal dysgenesis (gonads don't develop) / one in 150,000 births
Hypospadias (urethral opening in perineum or along penile shaft) / one in 2,000 births
Hypospadias (urethral opening between corona and tip of glans penis) / one in 770 births
Total number of people whose bodies differ from standard male or female / one in 100 births
Total number of people receiving surgery to “normalize” genital appearance / one or two in 1,000 births
Source