My wife is 12 weeks 1 day pregnant. her gyn did vaginal and normal ultrasound. he said probably baby boy but need time to confirm. is result accurate?

Consider: Waiting until a later ultrasound before picking out nursery wall paint. As your doctor indicated, "probably" is the operative word here and an ultrasound later will likely be more definitive.

The word probably: Says it all. 12 weeks is quite early, and the doctor's use of the word probably means it is better than 50-50 but nowhere near 90% likely. Fetal anatomy screening ultrasound at 18 to 21 weeks would provide a better opportunity to confirm the baby's gender.