Mismatch repair gene specifications to the ACMG/AMP classification criteria: Consensus recommendations from the InSiGHT ClinGen Hereditary Colorectal Cancer / Polyposis Variant Curation Expert Panel

Background It is known that gene- and disease-specific evidence domains can potentially improve the capability of the ACMG/AMP classification criteria to categorize pathogenicity for variants. We aimed to include gene–disease-specific clinical, predictive, and functional domain specifications to the ACMG/AMP criteria with respect to MMR genes. Methods Starting with the original criteria (InSiGHT criteria) developed by the InSiGHT Variant Interpretation Committee, we systematically addressed specifications to the ACMG/AMP criteria to enable more comprehensive pathogenicity assessment within the ClinGen VCEP framework, resulting in an MMR gene-specific ACMG/AMP criteria. Results A total of 19 criteria were specified, 9 were considered not applicable and there were 35 variations of strength of the evidence. A pilot set of 48 variants was tested using the new MMR gene-specific ACMG/AMP criteria. Most variants remained unaltered, as compared to the previous InSiGHT criteria; however, an additional four variants of uncertain significance were reclassified to P/LP or LB by the MMR gene-specific ACMG/AMP criteria framework. Conclusion The MMR gene-specific ACMG/AMP criteria have proven feasible for implementation, are consistent with the original InSiGHT criteria, and enable additional combinations of evidence for variant classification. This study provides a strong foundation for implementing gene–disease-specific knowledge and experience, and could also hold immense potential in a clinical setting. ### Competing Interest Statement Becky Milewski previously had a role with the pilot variant classification efforts in 2020/2021. She was previously an employee of GeneDx, LLC. Lauren Currie is an employee of GeneDx, LLC Ester Borras is an employee and shareholder of Invitae Corporation. John Paul Plazzer has previously consulted as curator for an external diagnostic testing company. ### Funding Statement JPP was supported by the Alan Watt and Chris Geyer Oncology Fellowship through The Royal Melbourne Hospital Foundation and NIH PA-18-591 Administrative Supplements to Promote Data Sharing in Cancer Epidemiology Studies. ABS was supported by NHMRC Funding (APP1104808). Grant funding for MKC: Cancer Council NSW, RG19-1. In Spain, this study has been partially funded by Ministerio de Ciencia e Innovacion, which is part of Agencia Estatal de Investigacion (AEI), through the Retos Investigacion grant, number PID2019-111254RB-I00, and La Marato de TV3 (202028-30). We also thank CERCA Programme / Generalitat de Catalunya for institutional support. MG was supported by Italian Ministry of Health RC 2022. KA and GY was supported by Japan Agency Medical Research and Development (AMED) under grant JP 18kk0205004, JSPS KAKENHI Grant Number JP18K07339 and JP22K07266. We would like to thank Ms. Lubaina Koti for editing the manuscript for language, structure, and accuracy. We acknowledge Marissa Rose for analysis of an early draft of the criteria. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Data is available in published literature (Pubmed IDs are provided in the databases listed here) or online open-access databases including: ClinVar , LOVD , and InSiGHT classification websites: [https://www.insight-database.org/classifications/mmr\_integrative\_eval.html][1] and Curated evidence will be available on I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Variant classifications are published in ClinVar () and curated evidence is available on the ClinGen Evidence Repository (). * ACMG : American College of Medical Genetics and Genomics AMP : Association for Molecular Pathology B : Benign BA : Benign Stand-Alone BS : Benign Strong BP : Benign Supporting ClinGen : Clinical Genome Resource CMMRD : constitutional mismatch repair deficiency GI : gastrointestinal gnomAD : Genome Aggregation Database FDA : Food and Drug Administration (United States) HCI : Huntsman Cancer Institute HGVS : Human Genome Variation Society IARC : International Agency for Research on Cancer IHC : immunohistochemistry InSiGHT : International Society for Gastrointestinal Hereditary Tumours IVS : intervening sequence (intron) LB : likely benign LP : likely pathogenic LOVD : Leiden Open Variation Database LS : Lynch syndrome MANE : matched annotation from National Center for Biotechnology Information and European Molecular Biology Laboratory and European Bioinformatics Institute MMR : mismatch repair (genes) MSI : microsatellite instability NGS : next generation sequencing NMD : nonsense–mediated mRNA decay P : Pathogenic PVS : Pathogenic Very Strong PS : Pathogenic Strong PM : Pathogenic Moderate PP : Pathogenic Supporting SVI WG : Sequence Variant Interpretation Working Group VCEP : variant curation expert panel VUS : variant of uncertain significance [1]: https://www.insight-database.org/classifications/mmr_integrative_eval.html