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For the core variables of IFS, Article 5 (3) of Regulation (EU) 2018/1091 states that "When a variable listed in Annex III has a low or zero prevalence in a Member State, the variable may be excluded from the data collection subject to the Member State concerned providing information duly justifying its exclusion to the Commission (Eurostat) in the calendar year preceding the reference year."
A similar statement for the module variables is included in Article 7 (9) of the same regulation. This information is sent to Eurostat as a separate data collection (NSNE).
For further details on the NSNE data collection, see chapter 3.10.