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Purpose: Predicting effects of genomic variants has become a real challenge in the diagnosis of rare human diseases. Holt-Oram syndrome (HOS) is an autosomal condition characterized by the association of radial and heart defects, due to variants in TBX5. Most variants are predicted to be truncating and result in haploinsufficiency. The pathogenicity of missense or splice variants is harder to demonstrate., Methods: Fourteen TBX5 variants of uncertain significance (VUS) (5 missense, 9 splice) and 6 likely pathogenic missense variants were selected for functional testing, depending on the variant-type (immunolocalization, western blot, reporter assays, minigene splice assays and RT-PCR). Results were compared with in silico predictions., Results: Functional tests allowed to reclassify 9/14 VUS in TBX5 as likely pathogenic, confirming their role in HOS. We demonstrated loss-of-function (n=8) or gain-of-function (n=1) for 9 of the 11 missense variants, whereas no functional impact was shown for the 2 variants: p.(Gly195Ala) and p.(Ser261Cys), as suggested by contradictory predictions of in silico approaches. Of 9 splice variants predicted to affect splicing by SpliceAI, we observed partial or complete exon skipping (n=6), intron retention (n=2) or exon shortening (n=1), inducing frame-shifting with premature stop codons., Conclusion: Bioinformatic and biological approaches are complementary, together with a good knowledge of clinical conditions, for accurate ACMG classification in human rare diseases., (Copyright © 2024. Published by Elsevier Inc.)