Please use this identifier to cite or link to this item: https://biore.bio.bg.ac.rs/handle/123456789/7205
Title: Comparison of the ABC and ACMG systems for variant classification
Authors: Houge, Gunnar
Bratland, Eirik
Aukrust, Ingvild
Tveten, Kristian
Žukauskaitė, Gabrielė
Sansovic, Ivona
Brea-Fernández, Alejandro J
Mayer, Karin
Paakkola, Teija
McKenna, Caoimhe
Wright, William
Keckarević-Marković, Milica 
Lildballe, Dorte L
Konecny, Michal
Smol, Thomas
Alhopuro, Pia
Gouttenoire, Estelle Arnaud
Obeid, Katharina
Todorova, Albena
Jankovic, Milena
Lubieniecka, Joanna M
Stojiljkovic, Maja
Buisine, Marie-Pierre
Haukanes, Bjørn Ivar
Lorans, Marie
Roomere, Hanno
Petit, François M
Haanpää, Maria K
Beneteau, Claire
Pérez, Belén
Plaseska-Karanfilska, Dijana
Rath, Matthias
Fuhrmann, Nico
Ferreira, Bibiana I
Stephanou, Coralea
Sjursen, Wenche
Maver, Aleš
Rouzier, Cécile
Chirita-Emandi, Adela
Gonçalves, João
Kuek, Wei Cheng David
Broly, Martin
Haer-Wigman, Lonneke
Thong, Meow-Keong
Tae, Sok-Kun
Hyblova, Michaela
den Dunnen, Johan T
Laner, Andreas
Issue Date: 22-May-2024
Rank: M21
Publisher: Nature Publishing Group
Journal: European journal of human genetics : EJHG
Abstract: 
The ABC and ACMG variant classification systems were compared by asking mainly European clinical laboratories to classify variants in 10 challenging cases using both systems, and to state if the variant in question would be reported as a relevant result or not as a measure of clinical utility. In contrast to the ABC system, the ACMG system was not made to guide variant reporting but to determine the likelihood of pathogenicity. Nevertheless, this comparison is justified since the ACMG class determines variant reporting in many laboratories. Forty-three laboratories participated in the survey. In seven cases, the classification system used did not influence the reporting likelihood when variants labeled as "maybe report" after ACMG-based classification were included. In three cases of population frequent but disease-associated variants, there was a difference in favor of reporting after ABC classification. A possible reason is that ABC step C (standard variant comments) allows a variant to be reported in one clinical setting but not another, e.g., based on Bayesian-based likelihood calculation of clinical relevance. Finally, the selection of ACMG criteria was compared between 36 laboratories. When excluding criteria used by less than four laboratories (<10%), the average concordance rate was 46%. Taken together, ABC-based classification is more clear-cut than ACMG-based classification since molecular and clinical information is handled separately, and variant reporting can be adapted to the clinical question and phenotype. Furthermore, variants do not get a clinically inappropriate label, like pathogenic when not pathogenic in a clinical context, or variant of unknown significance when the significance is known.
URI: https://biore.bio.bg.ac.rs/handle/123456789/7205
ISSN: 10184813
DOI: 10.1038/s41431-024-01617-8
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