"How come you want to learn English?" <--This is very common in everyday conversation in the US.
"How come" is the same as "Why".
Another way to ask the same question is:
Why do you want to learn English?There is only a subtle difference; sometimes "how come" implies that the person is surprised; the person thinks that this is not common.
"how come" is asking for an explanation. (short for: How did this come about, that.. ?) It can be more emotional.
"why" is asking for a reason, or a purpose. It's more detached.
Mom: "You can't go outside today."
Child 1: "Why not?" <-- asking for a reason. (Just curious, maybe not really bothered by Mom's decision.)
Child 2: "How come?" <- needs an explanation. (Maybe the child disagrees with Mom and needs to be convinced.)