Conditional sentences usually consist of a subordinate if-clause and a main clause. The order of the clauses is optional, but if the if-clause is first, a comma is used to separate the two clauses:
You might have been accepted if you had applied earlier.
If you had applied earlier, you might have been accepted.
If the if-clause is first, we can use then in the main clause:
If you had applied earlier, then you might have been accepted.