Deductions - The amount of "personal" contributions you made - these are contributions made OUTSIDE your employer - not through payroll deduction. This amount appears on line 25 of Schedule 1 (Form 1040) and on line 2 on form 8889. Exception: If you carried over excess contributions from the previous year and this excess was successfully charged off against the current year contribution limit, then the amount of the carryover is added to line 25; however, because it is a carryover and not a current year contribution, it does not appear on line 2 of form 8889.
You do not see the code W amount in box 12 of your W-2 as a deduction because it was removed from Wages in boxes 1, 3, and 5 on your W-2 before your W-2 was printed. It's not a deduction because it was never in your income in the first place. No, this is not obvious (but you can confirm it with your employer).
Only the direct contributions will appear as a deduction (line 25 on Schedule 1, and on the HSA Summary under "Deductions").
