Literature DB >> 31479589

Overview of Specifications to the ACMG/AMP Variant Interpretation Guidelines.

Steven M Harrison1,2, Leslie G Biesecker3, Heidi L Rehm1,2,4.   

Abstract

The 2015 ACMG/AMP guidelines established a classification system for sequence variants; however, the broad scope of these guidelines necessitates specification of evidence types for specific genes or diseases of interest. Since publication of the guidelines, both general use and disease-focused specifications have emerged to aid in accurate application of ACMG/AMP evidence types. This article summarizes the approaches to, and rationale for, specifying three evidence categories (population frequency data, variant type and location, and case-level data), including available resources and a quantitative framework that can inform the specification process.
© 2019 by John Wiley & Sons, Inc. © 2019 John Wiley & Sons, Inc.

Entities:  

Keywords:  ACMG/AMP guidelines; clinical genetics; variant interpretation

Mesh:

Year:  2019        PMID: 31479589      PMCID: PMC6885382          DOI: 10.1002/cphg.93

Source DB:  PubMed          Journal:  Curr Protoc Hum Genet        ISSN: 1934-8258


  24 in total

1.  Multidimensional structure-function relationships in human β-cardiac myosin from population-scale genetic variation.

Authors:  Julian R Homburger; Eric M Green; Colleen Caleshu; Margaret S Sunitha; Rebecca E Taylor; Kathleen M Ruppel; Raghu Prasad Rao Metpally; Steven D Colan; Michelle Michels; Sharlene M Day; Iacopo Olivotto; Carlos D Bustamante; Frederick E Dewey; Carolyn Y Ho; James A Spudich; Euan A Ashley
Journal:  Proc Natl Acad Sci U S A       Date:  2016-05-31       Impact factor: 11.205

2.  Recommendations for interpreting the loss of function PVS1 ACMG/AMP variant criterion.

Authors:  Ahmad N Abou Tayoun; Tina Pesaran; Marina T DiStefano; Andrea Oza; Heidi L Rehm; Leslie G Biesecker; Steven M Harrison
Journal:  Hum Mutat       Date:  2018-09-07       Impact factor: 4.878

3.  ClinGen--the Clinical Genome Resource.

Authors:  Heidi L Rehm; Jonathan S Berg; Lisa D Brooks; Carlos D Bustamante; James P Evans; Melissa J Landrum; David H Ledbetter; Donna R Maglott; Christa Lese Martin; Robert L Nussbaum; Sharon E Plon; Erin M Ramos; Stephen T Sherry; Michael S Watson
Journal:  N Engl J Med       Date:  2015-05-27       Impact factor: 91.245

4.  Gene-specific criteria for PTEN variant curation: Recommendations from the ClinGen PTEN Expert Panel.

Authors:  Jessica L Mester; Rajarshi Ghosh; Tina Pesaran; Robert Huether; Rachid Karam; Kathleen S Hruska; Helio A Costa; Katherine Lachlan; Joanne Ngeow; Jill Barnholtz-Sloan; Kaitlin Sesock; Felicia Hernandez; Liying Zhang; Laura Milko; Sharon E Plon; Madhuri Hegde; Charis Eng
Journal:  Hum Mutat       Date:  2018-11       Impact factor: 4.878

5.  Reassessment of Mendelian gene pathogenicity using 7,855 cardiomyopathy cases and 60,706 reference samples.

Authors:  Roddy Walsh; Kate L Thomson; James S Ware; Birgit H Funke; Jessica Woodley; Karen J McGuire; Francesco Mazzarotto; Edward Blair; Anneke Seller; Jenny C Taylor; Eric V Minikel; Daniel G MacArthur; Martin Farrall; Stuart A Cook; Hugh Watkins
Journal:  Genet Med       Date:  2016-08-17       Impact factor: 8.822

6.  Modeling the ACMG/AMP variant classification guidelines as a Bayesian classification framework.

Authors:  Sean V Tavtigian; Marc S Greenblatt; Steven M Harrison; Robert L Nussbaum; Snehit A Prabhu; Kenneth M Boucher; Leslie G Biesecker
Journal:  Genet Med       Date:  2018-01-04       Impact factor: 8.822

7.  The ACMG/AMP reputable source criteria for the interpretation of sequence variants.

Authors:  Leslie G Biesecker; Steven M Harrison
Journal:  Genet Med       Date:  2018-12       Impact factor: 8.822

8.  A framework for the interpretation of de novo mutation in human disease.

Authors:  Kaitlin E Samocha; Elise B Robinson; Stephan J Sanders; Christine Stevens; Aniko Sabo; Lauren M McGrath; Jack A Kosmicki; Karola Rehnström; Swapan Mallick; Andrew Kirby; Dennis P Wall; Daniel G MacArthur; Stacey B Gabriel; Mark DePristo; Shaun M Purcell; Aarno Palotie; Eric Boerwinkle; Joseph D Buxbaum; Edwin H Cook; Richard A Gibbs; Gerard D Schellenberg; James S Sutcliffe; Bernie Devlin; Kathryn Roeder; Benjamin M Neale; Mark J Daly
Journal:  Nat Genet       Date:  2014-08-03       Impact factor: 38.330

9.  A survey assessing adoption of the ACMG-AMP guidelines for interpreting sequence variants and identification of areas for continued improvement.

Authors:  Annie Niehaus; Danielle R Azzariti; Steven M Harrison; Marina T DiStefano; Sarah E Hemphill; Ozlem Senol-Cosar; Heidi L Rehm
Journal:  Genet Med       Date:  2019-01-23       Impact factor: 8.822

10.  Using high-resolution variant frequencies to empower clinical genome interpretation.

Authors:  Nicola Whiffin; Eric Minikel; Roddy Walsh; Anne H O'Donnell-Luria; Konrad Karczewski; Alexander Y Ing; Paul J R Barton; Birgit Funke; Stuart A Cook; Daniel MacArthur; James S Ware
Journal:  Genet Med       Date:  2017-05-18       Impact factor: 8.822

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  25 in total

1.  An all-encompassing variant classification system proposed.

Authors:  Philippe M Campeau
Journal:  Eur J Hum Genet       Date:  2021-10-29       Impact factor: 4.246

2.  A calibrated functional patch-clamp assay to enhance clinical variant interpretation in KCNH2-related long QT syndrome.

Authors:  Connie Jiang; Ebony Richardson; Jessica Farr; Adam P Hill; Rizwan Ullah; Brett M Kroncke; Steven M Harrison; Kate L Thomson; Jodie Ingles; Jamie I Vandenberg; Chai-Ann Ng
Journal:  Am J Hum Genet       Date:  2022-06-09       Impact factor: 11.043

3.  Novel Variant Expands the Clinical Spectrum of CUX2-Associated Developmental and Epileptic Encephalopathies.

Authors:  Feng Zhang; Fuwei Li; Fujian Chen; Jinrong Huang; Qiong Luo; Xilong Du; Jiapeng Zhou; Weiyue Gu; Kaishou Xu
Journal:  Front Genet       Date:  2022-07-01       Impact factor: 4.772

4.  Novel Heterozygous Missense Variant in GRIA4 Gene Associated With Neurodevelopmental Disorder With or Without Seizures and Gait Abnormalities.

Authors:  Hua Wang; Jiatong Liu; Fuwei Li; Ziteng Teng; Mingyu Liu; Weiyue Gu
Journal:  Front Genet       Date:  2022-04-20       Impact factor: 4.772

5.  Clinical Interpretation of Sequence Variants.

Authors:  Junyu Zhang; Yanyi Yao; Haixian He; Jun Shen
Journal:  Curr Protoc Hum Genet       Date:  2020-06

Review 6.  Genomic Screening for Malignant Hyperthermia Susceptibility.

Authors:  Leslie G Biesecker; Robert T Dirksen; Thierry Girard; Philip M Hopkins; Sheila Riazi; Henry Rosenberg; Kathryn Stowell; James Weber
Journal:  Anesthesiology       Date:  2020-12-01       Impact factor: 7.892

Review 7.  Variant interpretation using population databases: Lessons from gnomAD.

Authors:  Sanna Gudmundsson; Moriel Singer-Berk; Nicholas A Watts; William Phu; Julia K Goodrich; Matthew Solomonson; Heidi L Rehm; Daniel G MacArthur; Anne O'Donnell-Luria
Journal:  Hum Mutat       Date:  2021-12-16       Impact factor: 4.700

8.  Overcoming constraints on the detection of recessive selection in human genes from population frequency data.

Authors:  Daniel J Balick; Daniel M Jordan; Shamil Sunyaev; Ron Do
Journal:  Am J Hum Genet       Date:  2021-12-23       Impact factor: 11.043

9.  Rare Variants Associated with Arrhythmogenic Cardiomyopathy: Reclassification Five Years Later.

Authors:  Marta Vallverdú-Prats; Mireia Alcalde; Georgia Sarquella-Brugada; Sergi Cesar; Elena Arbelo; Anna Fernandez-Falgueras; Mónica Coll; Alexandra Pérez-Serra; Marta Puigmulé; Anna Iglesias; Victoria Fiol; Carles Ferrer-Costa; Bernat Del Olmo; Ferran Picó; Laura Lopez; Paloma Jordà; Ana García-Álvarez; Coloma Tirón de Llano; Rocío Toro; Simone Grassi; Antonio Oliva; Josep Brugada; Ramon Brugada; Oscar Campuzano
Journal:  J Pers Med       Date:  2021-02-26

10.  Combining evidence for and against pathogenicity for variants in cancer susceptibility genes: CanVIG-UK consensus recommendations.

Authors:  Alice Garrett; Miranda Durkie; Alison Callaway; George J Burghel; Rachel Robinson; James Drummond; Bethany Torr; Cankut Cubuk; Ian R Berry; Andrew J Wallace; Sian Ellard; Diana M Eccles; Marc Tischkowitz; Helen Hanson; Clare Turnbull
Journal:  J Med Genet       Date:  2020-11-18       Impact factor: 5.941

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