First of all, I don't use "via the phone" and I have never heard anyone else use it, so you can forget that one, in my opinion. "by the phone" cannot used to mean "by phone"; it is used to mean "near the phone", the same as with "by the table", "by the window", etc. While "over the phone" is understandable, I don't recommend it.
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I use the phrase ‘I spoke at the telephone ‘ when I report a conversation but only when writing it.