“How come?” is a question. It is very common in informal spoken English.
Meaning:
We say “how come?” to ask why something has happened.
We say “how come?” to ask why a particular situation exists.
“How come?“ expresses surprise by a situation.
Example:
Mark: Do you want to go to the cinema?
Jane: No.
Mark: How come?
Jane: I’m tired.
Form of “how come” – simple examples
If we want to simply ask “why?”, we can say “How come?”
Examples:
Jane: I’m not hungry.
Mark: How come?
Jane: I had a late breakfast.
David: Do you want to watch the football?
Mark: No.
David: How come?
Mark: I don’t like football.
Jane: I don’t like Clare.
Sarah: Really? How come?
Jane: She is rude!
Form of “how come” – full questions
Important:
“How come” is followed by a sentence in the affirmative form:
“How come” + sentence in affirmative form + “?”
Example: How come you are late?
Compare that to a “why” question whose form is the question form:
“Why” + sentence in question form + “?”
Example: Why are you late?
In the examples below, compare the difference in form of the “how come” questions with the “why” question. The meaning of each one is the same.
Examples:
How come you are giving me money?
Why are you giving me money?
How come you have sold your house?
Why have you sold your house?
How come you took my keys?
Why did you take my keys?
How come you are here?
Why are you here?
How come you went to London?
Why did you go to London?
Important: We do not conjugate “how come”. That means we never say “How came” or “How coming” to ask a question.
Example:
How came you went to London? 
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