The GMO Panel has previously assessed genetically modified (GM) carnation FLO‐40689‐6 and concluded that there is no scientific reason to consider that the import, distribution and retailing in the EU of carnation FLO‐40689‐6 cut flowers for ornamental use will cause any adverse effects on human health or the environment. On 27 October 2017, the European Commission requested EFSA to analyse new nucleic acid sequencing data and updated bioinformatics data for carnation FLO‐40689‐6 and to indicate whether the conclusions of the GMO Panel on the previously assessed GM carnation FLO‐40689‐6 remain valid. The new sequencing data indicated the correction of one nucleotide compared to the sequencing data originally provided. The new sequence was corrected by removal of one nucleotide from the polylinker region in locus 1. The removal of this base pair reported in the new nucleic acid sequencing data for carnation FLO‐40689‐6 has been already present in the original plant material used for the risk assessment. Thus, with the exception of bioinformatics analyses, the studies performed for the risk assessment of GM carnation FLO‐40689‐6 remain valid. The new sequencing data and the bioinformatic analyses performed on the new sequence, did not give rise to safety issues. Therefore, EFSA concludes that the original risk assessment of carnation FLO‐40689‐6 remains valid.