I think you are probably going to get varying answers to your question.
To me, they can be synonymous if the person you are asking still lives in the same place they were born, or grew up in.
Otherwise I think that they mean:
"Where are you from?" = "Where were you born?", or "where did you grow up?".
"Where do you live?" = "Where do you live now?".
Some people may strongly identify with where they live, and so may say that they are from the same place they live in now, even if they weren't born or grew up there.
Sometimes people clarify the original question to say "Where are you from originally?", to distinguish between "where were you born?" or "where did you grow up?", as opposed to "where do you live now?".