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Does my mother's estate need to go through probate in NY state if she only had a savings and checking account
A Will needs to be probated in New York if the estate is valued at $20,000 or more. The value of an estate is based only upon assets in the decedent's name alone. If all that your mother owned were joint bank accounts, then you would not need to probate the Will.
Your mother's joint accounts with you became yours at the instant of your mother's passing, by operation of law. If this was all the property she had, and there is absolutely nothing else, there is no reason to probate her will.