Families & Friends of Gays & Lesbians Support Group
This community is dedicated to parents, siblings, grandparents, other relatives and friends of someone who is either gay, lesbian, bisexual, transgender or questioning their sexual orientation. The purpose of this community is to help families and friendships grow and maintain positive relationships with gay sons, daughters, family or friends.
If you want to help educate yourself, and live in the USA, you may want to reach out to your nearest branch of PFLAG. PFLAG is an organization for the families and friends of gay individuals. These people have gone through what you have gone through and can help guide you to sensitively support your nephew on his journey.
They can also help you better wrap your head around certain concepts. For example, when you wrote "I have always knew that he was born with more female genes then male, like a girl stuck in a boys body". That actually doesn't describe someone who is gay, that describes someone who is transgender. I suspect you mean your nephew is gay. The difference between being gay and being transgender is that being gay means you are attracted to the same sex. Being transgender is about the sex you identify yourself as being and has nothing to do with attraction.
As for people your nephew can talk to, you and he might want to look into gay youth organizations. Maybe a GSA or something similar (try googling groups in your area). You can also set him up with a counselor or therapist to help him navigate his emotions if his mother consents.
Yes the reality is that at some point he will bring a boy home. It was a shock for my family when this happened with my first boyfriend, but they adapted. My brother who once had a panic attack a the idea of meeting my boyfriend, grew to love him as a friend. My elderly relatives who couldn't quite wrap their head around the situation still welcomed him with open arms at holidays and social functions. As long as there is love, there can be a solution.
Just keep making your nephew feel loved and safe and he will be ok. So long as he has someone that will love him exactly how he is, he stands the best chance of growing up happy and healthy.