If you have not yet gone through the Health Savings Account (HSA) section under Deductions and Credits, then your contribution will be shown as taxable on your return. After you have entered the information to verify that you were qualified to make the contribution to the HSA, then it will be removed from the taxable income.
Go to Deductions and Credits > Medical > 1099-SA, HSA, MSA and click Start or Update to get started.
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