If you made a contribution directly to you HSA custodian and not via a paycheck contribution through your employer, enter in the contribution in the Medical section for HSA under Deductions and Credits.
You'll answer questions about a 1099-SA (for distributions) first before arriving at the page 'Let's enter (name) HSA contribution'. Enter the amount you personally made not through your employer, then continue to the end answering questions regarding your HDHP.
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