Probably from older forms such as “How comes it that... ?” and “How did it come to be like this?”
Earlier historical forms:
- “How comes it then that this her cold so great is not dissolved through my so hot desire ...”, Edmund Spenser in “Sonnet 30”, 1611
- “But prithee how comes it to passe that you act Tragedies every day.”, Tho. Bates, “The Stage-players Complaint: In a Pleasant Dialogue Betweene Cane of the Fortune, and Reed of the Friers, Deploring Their Sad and Solitary Conditions for Want of Imployment, in this Heavie and Contagious Time of the Plague in London”, 1641
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- (idiomatic, informal) Why; why is it; for what reason or purpose?
- How come you didn’t leave when you had the chance?
“How come” differs from “why” in that the word order of the question is the same as that of a statement. Compare:
- You didn’t leave. (statement)
- How come you didn’t leave?
- Why didn’t you leave?
- ^ Hegeds, Irén; Fodor, Alexandra (2010): English Historical Linguistics 2010: Selected Papers from the Sixteenth International Conference on English Historical Linguistics, p. 179.