Generally, the amount in Box 1 is the Taxable Amount, even if Box 2a has 'Unknown' or the 'Taxable amount not determined' box is checked.
You could look at a prior year return to verify this.
The exception would be is if there is an amount in Box 5, which would indicate that part of the Box 1 amount was either Employee Contributions or Health Insurance premiums.
Be sure that you choose the CSF-1099-R entry screen.
Here's more info on Box 2a Unknown.
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