Variations are valued using the BOQ rates where they apply, rates derived from them, or agreed new rates. Until a variation is approved, the contractor carries the risk of doing work it may not be paid for.
Tracking variations separately from the original contract sum is what lets a contractor see the true revised contract value and explain the difference at the final account.
How Civova handles it
Civova records variations against each project with an approval step, so the revised contract value includes only approved changes.