'How come' is more colloquial than 'why', but they are not always used in the same way. If you asking if the two are interchangeable, the answer is : not exactly. 'How come' is a broader, more general question than 'why'. 'Why' means 'Tell me the reason for x ', while 'How come' means 'Tell me about the circumstances which brought about x.' For example, you come across an English teenager living in England and you discover that he speaks perfect Czech. You are surprised, so you say: 'How come you speak perfect Czech?' By this you mean 'Give me some more background information on this situation' ( 'Did you used to live in the Czech republic?' 'Is one of your parents Czech?' ) As you can see, it's a more general request for an explanation than simply 'Why'.

I think that "how come" is slang but it is often used instead of the word "why".

They are basically the same but "how come is not used as often