ACMG Guidelines for Genetic Variant Interpretation
Genetic variants should be classified into five categories according to the 2015 ACMG/AMP standards: pathogenic, likely pathogenic, variant of uncertain significance (VUS), likely benign, and benign, with only pathogenic and likely pathogenic variants being clinically actionable for medical management and cascade family testing. 1
Core Classification Framework
The ACMG/AMP guidelines utilize 28 evidence-based criteria to systematically evaluate variants, weighing multiple lines of evidence including population frequency data, computational predictions, functional studies, segregation analysis, and clinical phenotype correlation. 1, 2
Clinically Actionable Variants
Pathogenic (Class 5) and Likely Pathogenic (Class 4) variants are the only classifications that warrant clinical action, including initiation of disease-specific surveillance, risk-reducing interventions, and cascade genetic testing of at-risk family members. 1
These variants must have sufficient evidence demonstrating causality for the disease in question, incorporating data from multiple affected individuals, functional studies, and segregation within families when available. 1
Variants of Uncertain Significance (VUS)
VUS cannot be used for predictive cascade testing in family members and should not influence clinical management decisions. 1
VUS may be investigated further through cosegregation analysis in family members, parental testing to determine de novo status, or functional studies, but this should occur in research or specialized clinical contexts. 1
Approximately 11% of variants are reclassified over time, necessitating periodic reevaluation every few years. 1
Benign and Likely Benign Variants
- These variants do not contribute to disease risk and require no clinical action or family testing. 1
Disease-Specific Applications
Cardiovascular Genetic Testing
For inherited cardiovascular diseases, genetic testing should be performed first in the proband with clear phenotypic evidence of disease, not in asymptomatic relatives without a known familial variant. 1
Testing in phenotype-negative relatives without a known pathogenic variant in the family has very low diagnostic yield and will not change clinical screening recommendations. 1
The diagnostic yield varies by cardiomyopathy subtype: hypertrophic cardiomyopathy (30-60%), dilated cardiomyopathy (20-40%), and arrhythmogenic cardiomyopathy (40-60%). 1
Genetic testing panels must include detection of copy number variants (deletions/duplications), as these account for approximately 4% of pathogenic variants in desmosomal genes. 1
Cancer Predisposition Testing
For cancer susceptibility genes like ATM, heterozygous pathogenic variants confer moderate increased risks that require specific surveillance protocols rather than aggressive prophylactic interventions. 1
ATM heterozygotes have approximately 2-3 fold increased breast cancer risk, warranting enhanced surveillance with annual mammography and consideration of breast MRI based on individualized risk assessment using models like CanRisk. 1
Risk-reducing mastectomy is not routinely recommended for ATM heterozygotes but may be considered through shared decision-making when combined with strong family history. 1
Annual PSA testing beginning at age 40 is reasonable for male ATM heterozygotes given increased prostate cancer risk. 1
Cascade Testing Protocol
When a pathogenic or likely pathogenic variant is identified in a proband, targeted cascade testing should be offered to all first-degree relatives, with those testing negative released from lifelong clinical surveillance. 1
Genotype-Positive Relatives
Require disease-specific clinical screening at regular intervals (typically every 1-3 years depending on the condition and age). 1
Screening intervals may be extended in stable adult patients after multiple normal evaluations. 1
For cardiovascular conditions, baseline evaluation should include ECG, echocardiography, and ambulatory ECG monitoring starting at age 10 or earlier if clinically indicated. 1
Genotype-Negative Relatives
Can be discharged from serial clinical phenotype screening after baseline evaluation, as their disease risk returns to that of the general population. 1
Critical exception: If variant pathogenicity is later downgraded to VUS or benign, previously released family members must be recontacted and clinical surveillance reinitiated. 1
Families Without Identified Variants
- When genetic testing is negative or not performed in the proband, family members still require ongoing clinical phenotypic screening due to phenotypic heterogeneity and incomplete sensitivity of genetic testing. 1
Secondary/Incidental Findings
The ACMG recommends reporting pathogenic or likely pathogenic variants in 59 medically actionable genes (ACMG 59) when identified during exome or genome sequencing, unless patients opt out. 1
Thirty of these 59 genes relate to cardiovascular diseases. 1
VUS are not typically returned as incidental findings. 1
Secondary findings from research sequencing must be confirmed by Clinical Laboratory Improvement Amendments (CLIA)-certified clinical testing before clinical action. 1
Patients with secondary findings require comprehensive three-generation family history assessment and rigorous disease-appropriate phenotyping to determine if early signs of disease are present. 1
Critical Interpretation Principles
Context-Dependent Analysis
Genetic test results must always be interpreted in the context of the patient's clinical phenotype, family history, and gene-disease associations. 1
A pathogenic variant in an inappropriate gene for the patient's phenotype (e.g., KCNH2 variant in a patient with structural cardiomyopathy rather than isolated arrhythmias) may not explain the clinical presentation. 1
Segregation analysis within families provides critical evidence for variant pathogenicity, particularly for novel variants. 1
Multiple Pathogenic Variants
Two or more pathogenic variants occur in 3-5% of hypertrophic cardiomyopathy cases, up to 10% of arrhythmogenic cardiomyopathy families, and potentially higher frequencies in dilated cardiomyopathy. 1
Patients with multiple pathogenic variants typically have earlier onset, more severe disease, and worse outcomes including higher sudden cardiac death risk. 1
When multiple pathogenic variants are present in cancer predisposition genes (e.g., ATM and BRCA2), management follows recommendations for the gene conferring highest risk. 1
Limitations of Negative Testing
A negative genetic test (including VUS and benign variants) does not rule out a genetic cause, as diagnostic yield is incomplete across all conditions. 1
Uninformative results cannot be used for predictive cascade testing; family screening must continue using phenotypic evaluations. 1
Consider expanded testing strategies including larger panels, improved coverage for deletions/duplications, or exome sequencing in families with multiple affected individuals. 1
Reproductive Counseling
For autosomal dominant conditions, each offspring has a 50% chance of inheriting the pathogenic variant, though penetrance and severity vary. 1
Partner testing should be offered for autosomal recessive conditions, particularly with consanguinity or family history of the recessive disorder. 1
For ATM heterozygotes with unrelated, untested partners, the risk of having a child with ataxia-telangiectasia is approximately 1 in 800 (assuming 1 in 200 carrier frequency). 1
Reproductive options include preimplantation genetic diagnosis, prenatal genetic screening, and postnatal genetic testing, with genetic counseling to discuss benefits and limitations of each approach. 1
Variant Reclassification and Recontact
Laboratories should implement policies to periodically reevaluate variants as new evidence emerges, with mechanisms to recontact patients when classifications change. 1
Patients must be informed at the time of testing that variant interpretation may change over time and they may be recontacted with updated results. 1
Reevaluation should occur every few years or when new family/phenotype information becomes available. 1
Classification changes that affect family cascade testing strategies (upgrades to pathogenic/likely pathogenic or downgrades to VUS/benign) require immediate action to modify family screening approaches. 1