HSA contributions made through your employer (these appear on box 12 on your W-2 with a code of W) are removed from Wages on boxes 1, 3, and 5.
This is because HSA contributions made through the employer (whether employer contributions or contributions that you made through payroll deduction) are not subject to federal income tax, Social Security tax, nor Medicare tax.
Therefore, you don't see a deduction anywhere on your return, because the HSA contributions have already been removed from your income.
No, this is not obvious, but you are indeed getting the tax benefit for the HSA contributions.
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