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These figures are coming from the closing balance of Current VAT Payable and Current VAT Receivable GL accounts, you can check it from: Image Removedfrom Trial Balance or Statement of Account (Please refer to the manual: 7.7. Accounting: Reports )

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3) You can calculate the difference value and try to find the corresponding documents in both (Accounting and Tax reports). 

4) If you Entered or Deleted/Unposted documents backdated and document date is not within VAT Return period you will not see its reflection in current VAT Return, but it will be reflected in the Calculation of VAT Liability.

5) If you manually change some figures in VAT Return document, these changes will not appear in the Calculation of VAT Liability, it will be calculated according to the system's data not on the figures that you entered manually.