If the 5329 is showing the entire $5000 as 'excess', I suspect that you may have missed answering the questions about having a High Deductible Health Plan and not having other health insurance (such as Medicare) or answered them in a way that disqualified you from the HSA contributions.
If that is the case, and you DID have a High Deductible Health Plan and no other health insurance, when you amend your tax return, it will result in a refund.
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