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Why? A: "I'm sorry, but I'm not letting you go to the party tonight." B: "Aw, Mom! How come?"
How is it that, as in How come you're not attending the conference? Sometimes how come follows a statement and asks the question "why" or "in what way," as in You're not going? How come? The related phrase how so? functions the same way, as in You say she's changed her mind-how so?How come is short for how did it come about that and dates from the mid-1800s; how so, short for how is it so or how is it that , dates from about 1300.
How is it that; why: How come you're so late?