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Expanding ACMG variant classification guidelines into a general framework.

Emmanuelle Masson1,2, Wen-Bin Zou3,4, Emmanuelle Génin1

  • 1Univ Brest, Inserm, EFS, UMR 1078, GGB, 22 Avenue Camille Desmoulins, F-29200, Brest, France.

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|August 16, 2022
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Summary
This summary is machine-generated.

This study expands the American College of Medical Genetics and Genomics (ACMG) variant classification system to better classify genetic variants in complex diseases. The new framework accounts for a spectrum of clinical phenotypes and genetic effects, improving variant interpretation for both predisposing and causing genes.

Keywords:
ACMG guidelinesAllele frequency thresholdAllelic heterogeneityDisease prevalenceExome sequencingGenetic heterogeneityIncomplete penetranceMultifactorial/complex diseasePathogenicityVariant interpretation

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Area of Science:

  • Medical Genetics
  • Genomic Variant Classification
  • Disease Pathogenesis

Background:

  • The American College of Medical Genetics and Genomics (ACMG) provides five variant classification categories, widely used but limited for Mendelian diseases and dichotomous classifications.
  • Current ACMG guidelines struggle with the continuum of clinical phenotypes and genetic effects, necessitating an expanded framework.

Purpose of the Study:

  • To expand the ACMG variant classification guidelines into a general framework applicable to a broader range of diseases.
  • To incorporate the spectrum of clinical phenotypes and genetic effects into variant classification.
  • To develop a more nuanced system for classifying variants in both disease-predisposing and disease-causing genes.

Main Methods:

  • Utilized chronic pancreatitis (CP) as a disease model, encompassing both monogenic and multifactorial forms.
  • Analyzed four key CP genes (PRSS1, CFTR, SPINK1, CTRC) to categorize them as CP-causing or CP-predisposing.
  • Introduced "predisposing" and "likely predisposing" categories for CP-predisposing genes and extended ACMG categories with allele frequency and functional thresholds for CP-causing genes.

Main Results:

  • Classified CP genes into CP-causing (PRSS1, SPINK1) and CP-predisposing (CFTR, CTRC).
  • Developed a five-category system (predisposing, likely predisposing, uncertain significance, likely benign, benign) for predisposing genes.
  • Created a seven-category system (pathogenic, likely pathogenic, predisposing, likely predisposing, uncertain significance, likely benign, benign) for causing genes, incorporating allele frequency and functional thresholds.

Conclusions:

  • Proposed an expanded variant classification framework with five and seven categories for predisposing and causing genes, respectively.
  • This framework accommodates the continuum of genetic effects and clinical phenotypes, enhancing variant interpretation.
  • The enhanced classification system aims for maximal compliance with ACMG guidelines, facilitating practical application in medical genetics.