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Unfortunately, unless you think there was duress, coersion or some other reason for invalidating his choice of beneficiary under the annuity contract, you will not be able to successfully contest the payout. Think of it like a life insurance policy - the proceeds go the to beneficiaries in that contract and not through the will. Annuities do not pass through a will but rather to a named beneficiary by operation of contract. For this reason they can be given to the next generation without going through the often cumbersome and potentially expensive process of probate.
Another way to look at it: let's say your dad left an annuity to his friend Jack. Then he passsed, leaving his estate to you and your sister. You and your sister would not be able to defeat the annuity to his beneficiary Jack. Another way to look at it, in terms of the binding nature of contracts, even upon death: You dad buys a car and promises to pay $500/mo for 3 years. He passes after the first year, still owing 2 years of $500 payments. His estate owes this $24,000 (2 years of $500 payments. This debt, via contract, must be paid from his estate before the remainder gets divvied up between you and your sister.
Your dad' s decision to leave an annuity to your sister was within his rights and the will can not change that, it was already given to her. Again, without a reason to contest that contract, i.e. duress, not being of sound mind, etc. it will generally stand.
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