Box 1 of your W-2 will be lower than the amounts in boxes 3 and 5 by the amount of your pre-tax 401K contributions in box 12 code D.
So you recognize that the 401K contributions are pre-tax when you enter the box 1 number into your tax return.
(It is always possible that your individual W-2 has other codes or issues that affect these numbers.)
See also here.
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