It sounds like you need to amend your tax return and report your estimated tax payments in the correct spot. Here are the instructions to file an amended Form 1040.
Remove the 'withholding' you entered and instead enter the quarterly payments that you made in the Estimated Payments section. Where do I enter Estimated Payments?
If you originally put the correct amount in the wrong spot, there should not be any net $$ change to your tax return, but that should satisfy the IRS by moving the credit to the correct line on Form 1040.
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