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If all of the Health Savings Account (HSA) contributions were reported on your W-2 in box 12 with code W, there should not be a deduction for HSA showing on your return. Payroll deductions going to your HSA are pre-tax and not deducted.
You should go back through the HSA section of your return and double-check the entries to be sure that there is nothing entered as an additional HSA contribution. Pay close attention to the screen titled 'Let's enter your HSA contributions' and also the following screen asking about any additional contributions that your employer told you about. Answer Yes, and then be sure all the fields are blank.
Use these steps to return to the HSA section of your return:
Tried answering "yes" as suggested but did not remove the HSA deduction
Is it possible that on the screen "Let's enter [name]'s HSA contributions", you entered the amount of your payroll deductions as a "personal" contribution? This second field shows up on line 12 of Schedule 1 (1040).
However, as Annette noted above, any amount of contributions done through your employer - whether from your employer or from you by payroll deduction - do not appear as a deduction on line 12 of Schedule 1 (1040), because the code W amount in box 12 on your W-2 is removed from Wages in boxes 1,3, and 5 before your W-2 is printed.
I suggest that you remove all your HSA data and start over, in case some piece of data has gotten "stuck".
1. make a copy of your W-2(s) (if you don't have the paper copies)
2. delete your W-2(s) (use the garbage can icon next to the W-2(s) on the Income screen)
*** Desktop***
3. go to View (at the top), choose Forms, and select the desired form. Note the Delete Form button at the bottom of the screen.
*** Online ***
3. go to Tax Tools (on the left), and navigate to Tools->Delete a form
4. delete form(s) 1099-SA (if one), 8889-T, and 8889-S (if one)
5. go back and re-add your W-2(s), preferably adding them manually
6. go back and redo the entire HSA interview.
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