You will have to remove the excess contribution plus earnings by the due date of the return to avoid the 6% penalty. Please make a request with your bank to remove the excess contribution plus earnings.
You should amend your return. If you had some earned income, then you can keep part of the contribution and deduct this amount. You will enter the traditional IRA contribution and on the Penalty screen you will enter the contribution amount (no earnings) that you are removing by the due date.
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