Certain tax-advantaged items such as employer HSA contributions and health insurance premiums are removed from boxes 1, 3, and 5 on the W-2 before it is even printed, because they are not subject to either federal income tax, Social Security tax, nor Medicare tax. You cannot tell by looking at the W-2 if the employer removed these items, so you have to ask your payroll department or HR department.
Of course, you may notice that health insurance premiums can be found in box 12 with a code of DD and that HSA contributions are found in box 12 with a code of W, but even if you see these items, you still can't be sure that they were removed from boxes 1, 3, and 5 without asking.
On the other hand, as noted above, other tax advantage items are not subject to federal income tax but are subject to SS and Medicare taxes. A very common example is the 401(k). In this case, the amount in box 1 will be smaller than the amounts in boxes 3 and 5 by the amount of the contribution to the 401(k). Note that this contribution will also be listed in box 12 with a code of D.
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