You seem to be wondering how you should arrange the tenses in the main (first part) and subordinate clause (second part).
The answer to that is that it depends on what you want to say, as the other commenter said. The only case that is not likely is past tense in the main clause ("was because") combined with present tense in sub-clause.
In case you're not aware, please note that "could" and "might" in "It could/might be because ..." doesn't mean a past tense but just adds uncertainty. They are essentially in the present tense just like "is", so you don't have to change the tense in the sub-clause just because you have "could" or "might".
Some examples:
1A) It IS because he IS angry at me (that he's not calling me). (present-present)
1B) It MIGHT/COULD BE because he IS angry at me (that he's not calling me). (present-present)
2) It IS/MIGHT BE because we HAD plentiful rain in summer (that the crop yield is good). (present-past)
3A) It WAS because we HAD plentiful rain in summer (that the crop yield was good last year). (past-past)
3B) It MIGHT HAVE BEEN because we HAD plentiful rain in summer (that the crop yield was good last year). (past-past)
In (2), the event in the sub-clause was in the past (plentiful rain in summer), but that event is the reason for a present situation (good crop yield now), so the main clause's tense is in the present.
In (3), both the main and sub-clause are about a past event with no apparent connection to the present, so we put the main clause's tense in the past as well.
To put an uncertain reason (might/could be) in the past, we use the "might/could have been" form, which indicate that it was a probable, not certain reason.
You can see that all cases except "past-present" is possible depending on whether you're talking about the reason for a present or past situation, cause by a present or past event.