Yes, a personal contribution to an HSA would be separate from an elective deferral.
An 'elective deferral' contribution to an HSA through your employer would be shown on your W-2, in Box 12, with a Code W. If you made a contribution to your HSA on your own, that would be a 'personal contribution' and you would report that amount in TurboTax.
Your elective deferral amount is picked up when you enter your W-2.
Here's more info on HSA Contributions.
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