HSA contributions that are made through your employer - whether the employer's contribution or your contribution by payroll deduction - is reported in box 12 on you W-2 with a code of W.
Most taxpayers are unaware that this code W amount is removed from Wages in Boxes 1, 3, and 5 before your W-2 is printed. The reason why you don't see a deduction for HSA contributions in this case is because the HSA contributions were never in your income in the first place.
You can also make direct HSA contributions to your HSA, that is, by not going through your employer. The direct contributions DO appear as a deduction on your tax return, on line 12 on Schedule 1 (1040).
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