Repository logo
 
Publication

Comparison of the ABC and ACMG systems for variant classification

2024-05-22Journal article Open access
Simple item page
dc.contributor.authorHouge, Gunnar
dc.contributor.authorBratland, Eirik
dc.contributor.authorAukrust, Ingvild
dc.contributor.authorTveten, Kristian
dc.contributor.authorŽukauskaitė, Gabrielė
dc.contributor.authorSansovic, Ivona
dc.contributor.authorBrea-Fernández, Alejandro J.
dc.contributor.authorMayer, Karin
dc.contributor.authorPaakkola, Teija
dc.contributor.authorMcKenna, Caoimhe
dc.contributor.authorWright, William
dc.contributor.authorMarkovic, Milica Keckarevic
dc.contributor.authorLildballe, Dorte L.
dc.contributor.authorKonecny, Michal
dc.contributor.authorSmol, Thomas
dc.contributor.authorAlhopuro, Pia
dc.contributor.authorGouttenoire, Estelle Arnaud
dc.contributor.authorObeid, Katharina
dc.contributor.authorTodorova, Albena
dc.contributor.authorJankovic, Milena
dc.contributor.authorLubieniecka, Joanna M.
dc.contributor.authorStojiljkovic, Maja
dc.contributor.authorBuisine, Marie-Pierre
dc.contributor.authorHaukanes, Bjørn Ivar
dc.contributor.authorLorans, Marie
dc.contributor.authorRoomere, Hanno
dc.contributor.authorPetit, François M.
dc.contributor.authorHaanpää, Maria K.
dc.contributor.authorBeneteau, Claire
dc.contributor.authorPérez, Belén
dc.contributor.authorPlaseska-Karanfilska, Dijana
dc.contributor.authorRath, Matthias
dc.contributor.authorFuhrmann, Nico
dc.contributor.authorferreira, Bibiana
dc.contributor.authorStephanou, Coralea
dc.contributor.authorSjursen, Wenche
dc.contributor.authorMaver, Aleš
dc.contributor.authorRouzier, Cécile
dc.contributor.authorChirita-Emandi, Adela
dc.contributor.authorGonçalves, João
dc.contributor.authorKuek, Wei Cheng David
dc.contributor.authorBroly, Martin
dc.contributor.authorHaer-Wigman, Lonneke
dc.contributor.authorThong, Meow-Keong
dc.contributor.authorTae, Sok-Kun
dc.contributor.authorHyblova, Michaela
dc.contributor.authorDunnen, Johan T. den
dc.contributor.authorLaner, Andreas
dc.date.accessioned2024-09-06T13:06:42Z
dc.date.available2024-09-06T13:06:42Z
dc.date.issued2024-05-22
dc.description.abstractThe 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.eng
dc.identifier.doi10.1038/s41431-024-01617-8
dc.identifier.eissn1476-5438
dc.identifier.issn1018-4813
dc.identifier.urihttp://hdl.handle.net/10400.1/25859
dc.language.isoeng
dc.peerreviewedyes
dc.publisherSpringer Science and Business Media LLC
dc.relation.ispartofEuropean Journal of Human Genetics
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectLoint consensus recommendation
dc.subjectMedical genetics
dc.subjectAmerican college
dc.subjectAssociation
dc.subjectStandards
dc.subjectGenomics
dc.titleComparison of the ABC and ACMG systems for variant classification
dc.typejournal article
dspace.entity.typePublication
oaire.citation.endPage863
oaire.citation.issue7
oaire.citation.startPage858
oaire.citation.titleEuropean Journal of Human Genetics
oaire.citation.volume32
oaire.versionhttp://purl.org/coar/version/c_970fb48d4fbd8a85
person.familyNameferreira
person.givenNameBibiana
person.identifier.ciencia-idA311-E925-09C5
person.identifier.orcid0000-0003-4772-9395
relation.isAuthorOfPublicationc928b692-bf43-4e45-929b-cba3517a966d
relation.isAuthorOfPublication.latestForDiscoveryc928b692-bf43-4e45-929b-cba3517a966d

Files

Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
Comparison of the ABC.pdf
Size:
994.8 KB
Format:
Adobe Portable Document Format
Download
License bundle
Now showing 1 - 1 of 1
No Thumbnail Available
Name:
license.txt
Size:
3.46 KB
Format:
Item-specific license agreed upon to submission
Description:
Download

Collections

ABC2-Artigos (em revistas ou actas indexadas)