No part of the entry process for a Form 1099-R asks for this, including if the contribution was made as a QCD by an in-kind transfer of stock. If the contribution is a QCD, it is not reportable in the section for Charitable Donations under Deductions & Credits.
Is this contribution not a QCD such that it must be entered as an ordinary charitable contribution deductible on Schedule A instead? If so, the Form 1099-R would be reported on your tax return as a taxable distribution from the IRA to you, and a subsequent charitable contribution to the church. In that case, your basis in the shares in your possession is the value of the shares distributed and the holding period begins on that date. Under this scenario I assume that the donation was made less than a year after distribution from the IRA, so the holding period would be short-term.
