Box 2a of Form 1099-R should match whatever is shown on your paper Form 1099-R. If it is blank, then leave it blank. The taxable amount will be calculated based on your other entries in that section of your return.
With regard to the standard deduction being used even though you have many more itemized deductions to claim, if the bottom line income tax calculation is the same using either the standard deduction or itemized deductions, then the standard deduction will be used by TurboTax. There is no additional benefit to using itemized deductions and no need to file unnecessary forms with your return.
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