When you enter the Form 1099-Int you will have an option to indicate that it is not taxable. You will see a screen that says Do any of these uncommon situations apply? To which you can check the box that says I need to adjust the interest reported on my form. The next screen will say Tell us about your interest adjustment to which you can enter the amount to be reduced and choose a reason for the reduction (other reasons in this instance). The interest will not appear as taxable on your tax return.
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