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How can I determine if my refund was accurately filed? WheresMyRefund says it was accepted but the transcript says not filed.

It has been nearly 90 days since filing and my IRS transcript says nothing is filed. I've spent nearly 6+ hours on the phone trying to just ask the question to the IRS but they just hang up. Initially my filing was rejected because turbo tax left out a document/question but that was rectified 2 days later and that return was accepted.
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How can I determine if my refund was accurately filed? WheresMyRefund says it was accepted but the transcript says not filed.

Call the IRS: 1-800-829-1040 hours 7 AM - 7 PM local time Monday-Friday
When calling the IRS do NOT choose the first option re: "Refund", or it will send you to an automated phone line.
So after first choosing your language, then do NOT choose Option 1 (refund info). Choose option 2 for "personal income tax" instead.
Then press 1 for "form, tax history, or payment".
Then press 3 "for all other questions."
Then press 2 "for all other questions."
- When it asks you to enter your SSN or EIN to access your account information, don't enter anything.
- After it asks twice, you will get another menu.

Press 2 for personal or individual tax questions.
Then press 3 for all other inquiries
It should then transfer you to an agent.

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