The 1099-R that you received has been provided to the IRS. The IRS is going to review your return and match it to your tax documents (1099-R) and when you report a taxable amount other than what is on the form the IRS is going to make the change to your return to match the 1099-R and then notify you of the change.
The proper way to make the correction is to have a corrected 1099-R prepared and filed with the IRS by the payer.
Making the change on your own and e-filing your return may result in a delay in processing your return and receiving your refund, along with the potential the IRS makes adjustments that will adjust your refund.
