Yes, you can still deduct it. Often origination fees are not included in the Form 1098. It goes in the same area as the mortgage interest.
You can deduct any interest, property taxes, and most mortgage insurance premiums that are reported on the Form 1098 Mortgage Interest statement. You can also deduct any interest or property taxes from the settlement statement that are not already reported on the Form 1098 and not "pre-paid" and held in escrow.
Additionally, you can deduct qualified points paid on a mortgage and qualified mortgage insurance premiums. (Points can also be called loan origination fees, maximum loan charges, discount points, or loan discount.)
Where do I enter my 1098 mortgage interest statement?
https://ttlc.intuit.com/replies/4793767
Here's an alternate method to get there:
If in the Closing Disclosure the processing and underwriting fees are specificanlly listed under Origination Charges can the sum be deducted as Origination Fees? Assume lender's provided 1098 included only points of $2. There are three lines items like below (amounts are samples focusing more on descriptions).
Section: Loan Costs
A. Origination Charges = $4
1. 1% of Loan Amount (Points) = $2
2. Processing Fees = $1
3. Underwriting Fees = $1
Can the total of $4 be deducted or only $2 stated as points paid on 1098?