In 2015, the ACMGâAMP guidelines provided a general procedure for the objective and reproducible classification of genomic variants. While the benefits of this framework are of major importance, its adaptation for locusâspecific use is needed. Multiple Endocrine Neoplasia type 1 (MEN1) occurs due to inactivating mutations in the tumour suppressor gene MEN1, including 20% of missense variants. The classification of these variants may be extremely challenging. Here, we compared the interpretation of the 122
MEN1 missense variants, identified in the French population over the past 15 years by the TENGEN network (French oncogenetics network of neuroendocrine tumors) versus by using the ACMGâAMP guidelines, and analyzed the causes of discordance. A total of 59.8% of missense variants were termed as (likely)âpathogenic variants by TENGEN versus only 28.7% using ACMGâAMP guidelines. Actually, 53.4% (39/73) of TENGEN (likely)âpathogenic variants were declassified in variant of uncertain significance (VUS) by using ACMGâAMP guidelines, thereby affecting the clinical management of patients and their families. Twenty of these ACMGâAMP VUS were found in patients with a clinically authentic MEN1 disease. Here, TENGEN proposes adjustments to the ACMGâAMP framework for the interpretation of
MEN1 missense variants. These propositions merge both the classification systems, and are particularly interesting, as
MEN1 is included in the ACMG secondary findings list for reporting in clinical genomic sequencing.