Assuming the context is appropriate I think an acceptable way to ask is “what’s your heritage” - imo the important thing is not to sound like you’re assuming they’re a foreigner just because their ethnicity / appearance. I think asking about someone’s family story or where their family is from is also a good way to ask because it’s clear you’re asking about their family and not assuming that it has bearing on the person’s upbringing.
It also can be really confusing when you’re a mixed and natural born citizen and you have no idea if “where are you from” is just smalltalk and they want to know where you grew up or if they’re assuming based on your appearance that you immigrated and assuming that the answers to “where did you grow up” and “where are your ancestors from” are 1 and the same. So personally I like when people are more specific because when asked where I’m from I’m just going to ask if they mean where I grew up or where my parents are from.