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HMRC internal manual

VAT Default Interest Manual

From
HM Revenue & Customs
Updated
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Commercial restitution: Differences in stagger or return length between taxpayers

There will be cases where output tax could be recovered by a third party as input tax, but the third party is on a different stagger or length of accounting period from the taxpayer you are assessing. 

Normally you need not take account of a difference of stagger or length of accounting period between taxpayers when considering if interest should apply.