Genetic Variant Interpretation Tool (ACMG/AMP)

French translation

Posted in PHENO-product-level-category

This is a translation into French of the tool which can be found at:

Phenosystems is grateful to Linda Jo Bone Jeng, MD, PhD, FACMG This email address is being protected from spambots. You need JavaScript enabled to view it. for permission to reproduce a French translation of their tool and to Dr Pascale Benlian, MD This email address is being protected from spambots. You need JavaScript enabled to view it.for providing the French translation.

To aid our variant interpretation process, we created an openly-available online tool to efficiently classify variants based on the evidence categories outlined in the article: Richards, et al. Standards and guidelines for the interpretation of sequence variants. 2015. This site displays the evidence categories and descriptions from Table 3 and Table 4 with simple checkboxes for selecting appropriate criteria. The site then incorporates the algorithm in Table 5 to automatically assign the pathogenicity or benign impact based on the selected evidence categories. Since our process often requires analyzing multiple variants per patient, we have also allowed the option of aggregating each variant into an exportable table at the foot of the website for easy documentation of the variant review process for our records. Although this tool is based on the ACMG/AMP Standards and Guidelines, it is not affiliated with ACMG, AMP, or any of the authors of the publication.

Patient ID:
Variant ID:

PVS1 Allèle Nul / Epissage / Grand Réarrangement / Perte Codon initiation

PS1 Récurrence d'une mutation sur un codon produisant le même Acide Aminé
PS2 Mutation De-Novo démontrée
PS3 Effet Fonctionnel Démontré (Preuves in-vivo/in-vitro)
PS4 Présente dans >=2 familles, BDD Spécifique de Maladie/ Publications (Preuve in-vivo)
PP1 Coségrégation chez >=10 membres d'une famille (Preuve in-vivo)

PM1 Domaine Fonctionnel Caractérisé (Preuves in-vivo/in-vitro)
PM2 Absent ou < 0,01 dans BDD Population Générale (Preuve in-vivo)
PM3 Homozygote ou Hétérozygote Composite dans maladie récessive (Preuve in-vivo)
PM4 Mutation In-Frame / Perte de codon Terminal (Preuve in-vivo)
PM5 Récurrence sur le même Acide Aminé (Preuve in-vivo)
PM6 Possible De Novo (parents non disponibles)
PP1 (Moderate evidence) Cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease

PP1 Coségrégation chez plusieurs membres d'une famille (Preuve in-vivo)
PP2 Nombreuses Mutations Faux-Sens Causales Décrites à ce Locus (Preuve in-vivo)
PP3 Haute Conservation Structurale (Preuve in-silico)
PP4 Phénotype Typique de la Maladie associé au Locus (Preuve in-vivo)
PP5 Rapportée Pathogène dans BDD Spécifique de Maladie mais Non Publiée (Preuve in-vivo)

BP1 Faux Sens alors que surtout Mutations Non-Sens Causales Décrites à ce Locus (Preuve in-vivo)
BP2 Présente en Cis d'une mutation Pathogène à ce locus (Preuve in-vivo)
BP3 In-frame au sein d'un domaine répété (Preuve in-silico)
BP4 Conservation Structurale Modérée (Preuve in-silico)
BP5 Présence en association à une mutation pathogène à un autre Locus (Preuve in-vivo)
BP6 Rapportée Bénigne dans BDD Spécifique de Maladie mais Non Publiée (Preuve in-vivo)
BP7 Variant Synonyme sur résidu peu conservé avec possible effet sur épissage (Preuve in-silico)

BS1 Fréquence allélique > fréquence de la maladie dans la population (Preuve in-vivo)
BS2 Observée chez >1 sujet sain (Preuve in-vivo)
BS3 Non fonctionalité démontrée (Preuve in-vitro/in-vivo)
BS4 Absence de coségrégation avec le phénotype dans la famille (Preuve in-vivo)

BA1 SNP présent avec un fréquence > 5% en population générale (Preuve in-vivo)

Sequencing artifact as determined by depth, quality, or other previously reviewed data

Variant Classification:

Patient Name
VariantEffectEvidenceTo delete

Download Table as CSV

Please note that the text of the variant evidence has been pulled directly from Richards, et al. Genet Med. 2015 May;17(5). This site does not claim authorship of any of the variant evidence descriptions.

This tool is based on the published ACMG/AMP Standards and Guidelines [Genet Med (2015)]. Anyone using this tool should be familiar with that publication. Individuals or institutions choosing to use this tool for clinical variant classification purposes assume legal responsibility for the consequences of its use. The authors make no warranty, express or implied, nor assume any legal liability or responsibility for any purpose for which the tool is used.

Please cite the following when using this tool in publications:
Kleinberger J, Maloney KA, Pollin TI, Jeng LJ. An openly available online tool for implementing the ACMG/AMP standards and guidelines for the interpretation of
sequence variants. Genet Med. 2016 Mar 17. doi: 10.1038/gim.2016.13. [Epub ahead of print] PubMed PMID: 26986878.

For use in publications, please contact:
Linda Jeng, MD, PhD, FACMG
This email address is being protected from spambots. You need JavaScript enabled to view it.

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