Boxes 5 and/or 9 would have entries in order for a taxable amount to be less than the gross amount. When after-tax dollars are contributed to a retirement account, they are dribbled out over time as reductions in the amount of the distribution that is taxable. The annuity calculation is really also a pension calculation. Try using the Bogart Pension/Annuity Tool yourself to see if it duplicates your taxable number. There is a similar thing for IRA's that have a comparable after-tax basis. IRS Form 8606 is then used to calculate the reduction.
