Is How come a phrase? What does it mean? Is it formal or informal? British or American?
Can I use it in anywhere?
How come is a fixed phrase with fixed uses of its own.
It means, as you have divined, why, and may be used, like why, either as the head of a noun phrase, or as a bare interrogative, or as an interrogative head; but as an interrogative head it does not take ‘DO-support’—that is, it is followed by an ordinary clause in indicative form:
And that's why I went to the party. ... And that's how come I went to the party.
Why? .... How come?
Why did you go to the party? ... How come you went to the party?
It is never inflected: we never say ✲How came or ✲How has come or ✲How comes or anything of the sort.
How come is not used in formal writing or speech; it is distinctly casual.
I don't understand how that can be. Please be good enough to provide an explanation.
It is colloquial, and in some circumstances it might sound rude. As a foreign learner, you should avoid it yourself until you are confident about its use, but it's important for you to understand it.
"How come" is actually often seen as a more polite, less confrontational way of asking "why?" in standard American English. I encourage my adult ESL students to use it instead of WHY in most situations. Often when a person is asked WHY, they feel somewhat defensive, as if the person asking is challenging the action. In my experience, when a person is asked HOW COME instead of WHY it sounds more like the asker is simply, genuinely asking for help understanding the other person's reasoning rather than challenging it. That leads to a less defensive response and better communication overall. I believe students learning English should be taught HOW COME early in the language learning process, at the same time they are taught the basic question words WHO WHAT WHEN WHERE WHY and encouraged to use HOW COME in conversation rather than why. I'm surprised by the above comments that HOW COME has a stronger, more complex or rude meaning than WHY and should be avoided by inexperienced speakers. I'm going to think about that and see if I can come up with any evidence that this feeling is common. It is very different than my view of the phrase.
"How come" in questions is short for "How does/did/has it come + (that) clause. It is colloquial style. - How come your English is so good?
I'm not an expert on word history, but I do know that I heard this phrase more often in the South Eastern United States where I grew up more than I hear it in the South West where I have lived for 15 years. It may be best to avoid it outside the South East unless you hear other people using it.
Many have stately that it can be replaced with "why". In many cases, I would agree. However, it needs to have more words with it sometimes.
How come my knees pop when I stand up? Why do my knees pop when I stand up?
Or the verb may need to move as in this example.
How come my check engine light is on in my car? Why is my check engine light on in my car?
I would venture to say that the phrase means more than just "why". I think it may have been shortened from a phrase such as "how did this come to pass". Just a guess though based on my experience using this phrase in the South Eastern United States. Feel free to disagree.