If the payment of points was included in your W-2, then yes you can deduct the points. You can amend your original return, but wait until it is fully processed.
If you had a refund/tax payment due wait until
you receive the refund or the payment is processed.
https://ttlc.intuit.com/questions/1894381-how-to-amend-change-or-correct-a-return-you-already-filed
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