I know that 是谁打电话过来呢 means "who is calling?" but I don't know how to parse it:
- why is 是 at the beginning?
- not sure about the meaning of 过来. Is 电话过来 a standard combination?
- why 呢? I thought it is used for "what about...?" questions.
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This sentence has an abbreviated 的 in 是誰打電話過來的呢. 是～的 is a very common construction that you must remember; it is used for emphasis. In your sentence, you would like to emphasise who called. Basically, 誰打電話過來 (who called) is the question without any emphasis.
打～過來 should be seen together, not 電話過來. For details please see my explanation on the auxiliary verb 來 here. In general, 來 may (1) indicate an observed movement caused by the main verb (打) towards the speaker; or (2) the start (or in a more abstract sense, consequence) of the action caused by the main verb. Here, it emphasises someone called as if the call approached the speaker. A more semantically accurate translation of 打～過來 is 'to call here'.
Your statement on 呢 is irrelevant in this situation. While 嗎 is a question particle for yes/no questions, 呢 is a question particle for 5W1H words, in this case 'who'. Therefore,
是誰打電話過來的嗎（✖） 是誰打電話過來的呢（✓） Who is it that called? 是他打電話過來的呢（✖） 是他打電話過來的嗎（✓） Is it he who called?
[是谁] = [(it) is who]
打 = dials
电话 = phone
[打电话] = [makes phone call]
过 = over
来 = toward here
[过来] (verb particle indicates the direction of the verb)
[呢?] (particle indicate a question, but not a yes or no question )
是谁打电话过来 = who makes the phone call (coming in/ toward here) = who called (in) here?
是谁打电话过去 = who makes the phone call (going out/ toward there) = who called (out) there?