Genetically modified (GM) soybean 40-3-2 expresses a 5-enolpyruvylshikimate-3-phosphate synthase protein from Agrobacterium sp. strain CP4 (CP4 EPSPS), which confers tolerance to glyphosate. This event was previously assessed by the GMO Panel as a single event and as part of a two-event stack and was found to be as safe as its conventional counterparts and other appropriate comparators with respect to potential effects on human and animal health and the environment. On September 2021, the European Commission requested EFSA to evaluate a new bioinformatics study which revealed predicted genomic deletions at the insertion sites using the available soybean reference genome. Considering the variability of the soybean genome, with a number of structural variants such as presence/absence variants and copy number variants including genic regions, as well as the fact that a number of genes are present only in particular varieties, the GMO Panel concludes that comparing only to the reference genome does not allow to conclude that the transformation event resulted in gene loss. In support of this, the transcriptomic analysis did not show major differences in gene expression when comparing the soybean 40-3-2 with the most closely related conventional variety, indicating that the genetic redundancy may compensate for the potential gene loss. Moreover, the composition, phenotypic and agronomic analyses already assessed by the GMO Panel in previous opinions did not show differences between soybean 40-3-2 and its comparators suggesting that the potential gene loss may not have a significant phenotypic effect in soybean 40-3-2. For these reasons, the EFSA GMO Panel concludes that the new information provided by the applicant on soybean 40-3-2 does not alter EFSA's previous conclusions.