1. If it had not been for your call, I would have been late for school.

2. But for/Without your call, I would have been late for school.

3. Had it not been for your call, I would have been late for school.

4. If you had not called me, I would have been late for school.
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Are they all grammatical and the same in meaning?

Yes ... all are correct and mean about the same thing.