There are two ways to make a contribution to an HSA, one through your employer and the other directly to your HSA not though your employer.
If you make an HSA contribution directly to your HSA not through your employer, then this appears on line 12 on Schedule 1 (1040) as an adjustment to gross income.
If, however, either your employer made contributions to your HSA or you did through payroll deduction, then this total is reported in box 12 on your W-2 with a code of W.
NOTE: this amount was already removed from Wages in boxes 1, 3, and 5 before your W-2 was printed. That's why you don't see it as a deduction, because it was never in your income in the first place. Make sense?
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