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After you file
Form 8606 is not used to calculate the taxable portion of a pension distribution, it is used for IRAs.
When you enter the information from the Form 1099-R reporting the pension distribution, enter it just as the form was received. There will be a series of follow-up questions that you will answer where you will be able to enter the employee contributions and other information in order to determine the taxable amount of the distribution.
You will see questions such as whether the distribution came from a qualified plan, whether you received periodic payments, whether you began to receive the payments in 2017, and that you need to figure out how much of the distribution is taxable.
You will then see a screen where you can enter the annuity start date, the plan cost, the number of months received in 2017, and the death benefit exclusion. The plan cost is where you will enter the amount of employee contributions that were made. All of this information together will be used to calculate the taxable amount of the distribution.
Be sure to keep the information about the plan cost/employee contributions in your records.