Title: Interpreting Incidentally Identified Variants in Genes Associated With Heritable Cardiovascular Disease: A Scientific Statement From the American Heart Association
Abstract: HomeCirculation: Genomic and Precision MedicineVol. 16, No. 2Interpreting Incidentally Identified Variants in Genes Associated With Heritable Cardiovascular Disease: A Scientific Statement From the American Heart Association Free AccessReview ArticlePDF/EPUBAboutView PDFView EPUBSections ToolsAdd to favoritesDownload citationsTrack citationsPermissions ShareShare onFacebookTwitterLinked InMendeleyReddit Jump toFree AccessReview ArticlePDF/EPUBInterpreting Incidentally Identified Variants in Genes Associated With Heritable Cardiovascular Disease: A Scientific Statement From the American Heart Association Andrew P. Landstrom, Anwar A. Chahal, Michael J. Ackerman, Sharon Cresci, Dianna M. Milewicz, Alanna A. Morris, Georgia Sarquella-Brugada, Christopher Semsarian, Svati H. Shah, Amy C. Sturm and on behalf of the American Heart Association Data Science and Precision Medicine Committee of the Council on Genomic and Precision Medicine and Council on Clinical Cardiology; Council on Cardiovascular and Stroke Nursing; Council on Hypertension; Council on Lifelong Congenital Heart Disease and Heart Health in the Young; Council on Peripheral Vascular Disease; and Stroke Council Andrew P. LandstromAndrew P. Landstrom https://orcid.org/0000-0002-1878-9631 , Anwar A. ChahalAnwar A. Chahal , Michael J. AckermanMichael J. Ackerman , Sharon CresciSharon Cresci , Dianna M. MilewiczDianna M. Milewicz , Alanna A. MorrisAlanna A. Morris , Georgia Sarquella-BrugadaGeorgia Sarquella-Brugada , Christopher SemsarianChristopher Semsarian , Svati H. ShahSvati H. Shah , Amy C. SturmAmy C. Sturm and on behalf of the American Heart Association Data Science and Precision Medicine Committee of the Council on Genomic and Precision Medicine and Council on Clinical Cardiology; Council on Cardiovascular and Stroke Nursing; Council on Hypertension; Council on Lifelong Congenital Heart Disease and Heart Health in the Young; Council on Peripheral Vascular Disease; and Stroke Council Originally published27 Mar 2023https://doi.org/10.1161/HCG.0000000000000092Circulation: Genomic and Precision Medicine. 2023;16is corrected byCorrection to: Interpreting Incidentally Identified Variants in Genes Associated With Heritable Cardiovascular Disease: A Scientific Statement From the American Heart AssociationOther version(s) of this articleYou are viewing the most recent version of this article. Previous versions: March 27, 2023: Ahead of Print AbstractRapid advances in genetic technologies have led to expanding use of diagnostic, research, and direct-to-consumer exome and genome sequencing. Incidentally identified variants from this sequencing represent a significant and growing challenge to interpret and translate into clinical care and include variants in genes associated with heritable cardiovascular disease such as cardiac ion channelopathies, cardiomyopathies, thoracic aortic disease, dyslipidemias, and congenital/structural heart disease. These variants need to be properly reported, the risk of associated disease accurately assessed, and clinical management implemented to prevent or lessen the disease so that cardiovascular genomic medicine can become both predictive and preventive. The goal of this American Heart Association consensus statement is to provide guidance to clinicians who are called on to evaluate patients with incidentally identified genetic variants in monogenic cardiovascular disease genes and to assist them in the interpretation and clinical application of variants. This scientific statement outlines a framework through which clinicians can assess the pathogenicity of an incidental variant, which includes a clinical evaluation of the patient and the patient's family and re-evaluation of the genetic variant in question. Furthermore, this guidance underscores the importance of a multidisciplinary team to address these challenging clinical evaluations and highlights how clinicians can effectively interface with specialty centers.Diagnostic genetic testing has been a critical component of the evaluation of heritable monogenic cardiovascular disease (CVD) for >3 decades. These conditions include cardiac ion channelopathies, cardiomyopathies, heritable thoracic aortic disease, and familial dyslipidemias. With decreasing cost, increasing accessibility, and expanding clinical indications, exome sequencing (ES) and genome sequencing (GS) are becoming frontline diagnostic tools in a host of scenarios, including heterogeneous and atypical presentations of disease, unclear diagnoses resulting in a prolonged diagnostic odyssey, and the critically ill infant and child, among others.Although diagnostic genetic testing is performed when there is a clinical evaluation suggestive of a heritable CVD, ES and GS are frequently conducted for a primary indication unrelated to CVD but can uncover the presence of variants in CVD-associated genes. These so-called incidentally identified variants are often viewed as actionable markers of risk for disorders that confer a high degree of morbidity or mortality that may be prevented or reduced by clinical intervention. The American College of Medical Genetics and Genomics (ACMG) has provided guidance as to how these variants should be interpreted in the clinical arena. Specifically, variants that fall into actionable genes and are considered to be likely pathogenic or pathogenic (LP/P) are eligible to be reported back to the ordering clinician.1,2 ACMG defines these variants as secondary findings/variants. However, despite this paradigm-setting consensus, guidance as to how the referring clinician should incorporate this information into the evaluation and care of their patient for heritable CVD is lacking. For example, recent evidence suggests that the burden of incidentally identified genetic variants in CVD-associated genes is markedly higher than the prevalence of disease in the population. This highlights the diagnostic challenge in interpreting these variants to accurately predict the risk for disease development (ie, disease penetrance). Moreover, potentially actionable incidental variants are increasingly being identified outside of clinical ES and GS testing and in genes apart from the ACMG list such as in population genetic research studies or direct-to-consumer genetic testing. Thus, the goal of this scientific statement is to provide a comprehensive framework by which a clinician can interpret any incidentally identified CVD gene variant, incorporate this interpretation into a disease- and patient-specific cardiovascular evaluation, and arrive at a plan for patient, family, and variant follow-up.Existing LiteratureRecent expansion of the use of ES and GS for patients without clinical concern for heritable CVD has identified a growing number of incidentally identified variants in CVD-associated genes. This raises challenging questions related to the likelihood of disease risk for a given incidental variant and, if in a disease risk gene, how this risk should be incorporated into the evaluation and management of the individual. This scientific statement draws on existing orthogonal clinical practice guidelines, scientific statements, expert consensus statements, and key studies in the field to synthesize recommendations for these issues. Statements from the American Heart Association, American College of Cardiology, Association for Molecular Pathology, Clinical Pharmacogenetics Implementation Consortium, Heart Rhythm Society, ACMG, Heart Failure Society of America, European Society of Cardiology, European Association of Cardiovascular Imaging, European Heart Rhythm Association, Asian Pacific Heart Rhythm Society, Latin American Heart Rhythm Society, and Association of Inherited Cardiac Conditions were included. Literature that was in the English language and either human subject based or clinically focused was included. Because of the rapid evolution of genetic medicine, included studies were limited primarily to those published in or after 2010.Guidelines for Reporting of Incidental VariantsIncidental variants refer to rare variants identified that are not related to the phenotype or disease presentation for which the testing was ordered. Herein, we use the term incidental to include secondary variants, as defined by the ACMG, as well as variants found through various nonclinical means that may be reported to clinicians or patients. Although CVD gene–specific panels represent the typical diagnostic test of choice in the evaluation of heritable CVD, incidental variants are often identified when ES and GS testing is used for other clinical presentations. When this testing is performed on an individual without a priori concern for CVD, discerning the diagnostic relevance of these variants remains challenging. The ACMG published guidance on clinically actionable genes, which currently has 78 named genes.2 Of these, 42 (54%) are CVD related (Table 1). Specific genes relating to CVD are included as a result of a recognized increase in morbidity and mortality from sudden cardiac death, aortic dissection, and heart failure syndromes and the availability of established evidence-based treatments.3–7 It is important to note that this list is dynamic and will continue to evolve and that there is a significant lag phase between the ACMG panel of genes and what experts in the field consider actionable. These variants are referred to as secondary variants. The Centers for Disease Control and Prevention advised a 3-tier system for actionable genomic applications: tier 1 genes are supported by a base of synthesized evidence that supports that identification should alter management to prevent the disease; tier 2 genes are supported by synthesized evidence if insufficient to support routine implementation for informed decision-making (eg, pharmacogenomics); and tier 3 genes for which there is no evidence that a variant is actionable clinically, including cases in which there are evidence-based recommendations against use, or is not ready for routine implementation in practice (eg, polygenic risk scores).8 At present, familial hyperlipidemia–associated genes represent the only CVD-related condition in the Centers for Disease Control and Prevention tier 1 list, with the remainder being cancer-related genetic applications. This is likely to evolve toward the inclusion of additional CVD-related genes, including hypertrophic cardiomyopathy–associated genes.Table 1. Summary of CVD-Associated Genes With Yield of Incidentally Identified Variants by Disease Type*ACMG actionable genesCurrent genesMIMInheritance modeConsiderationsClinGen definitive or strong-evidence genes not included in ACMGDyslipidemia FHLDLRAPOBPCSK9143890144010603776SDADAD…Cardiomyopathy ACMPKP2DSPDSC2TMEM43DSG2609040607450610476604400610193ADJUP (strong)DES (moderate)PLN (moderate) DCMTNNT2LMNAFLNCTTNBAG3DESRBM20TNNC1601494115200617047604145613881604765613172611879ADHigh penetrance, extreme of phenotypeTruncating variantsSCN5A (definitive)MYH7 (definitive) HCMMYH7MYBPC3TNNI3TPM1MYL3ACTC1PRKAG2MYL2192600115197613690115196608751612098600858608758ADALPK3 (definitive)TNNT2 (definitive) included under DCM ACMG-73Restrictive/infiltrativeTTR105210ADHereditary transthyretin amyloidosisDefinitive for HCM FabryGLA301500XLOnly reported gene PompeGAA232300AROnly reported gene HHHFE235200ARNot yet curatedArrhythmia LQTS1 LQTS2 LQTS3KCNQ1KCNH2SCN5A192500613688603830ADCALM1 (definitive)CALM2 (definitive)CALM3 (definitive)TRDN (strong) BrS†SCN5A601144AD CPVTRYR2CASQ2TRDN604772611938615441ADARARCASQ2 and TRDN reportable in trans or apparently homozygous.TECRL (definitive)Thoracic aortic diseaseFBN1TGFBR1TGFBR2SMAD3ACTA2MYH11154700609192610168613795611788132900ADTGFB2MYLKLOXPRKG1 EDS (vascular)COL3A1130050ADIncluded with HTAD, not curated for EDSACM indicates arrhythmogenic ventricular cardiomyopathies; ACMG, American College of Medical Genetics and Genomics; AD, autosomal dominant; AR, autosomal recessive; BrS, Brugada syndrome; CPVT, catecholaminergic polymorphic ventricular tachycardia; DCM, dilated cardiomyopathy; EDS, Ehlers-Danlos syndrome; FH, familial hypercholesterolemia; HCM, hypertrophic cardiomyopathy; HH, hereditary hemochromatosis; HTAD, hereditary thoracic aortic disease (also known as familial thoracic aortic aneurysm and dissection); LQTS, long-QT syndrome; MIM, Mendelian Inheritance in Man; SD, semidominant; and XL, X-linked.* Based on current ACMG actionable genes (version 3.1).2 Although there are no genes associated with the development of isolated congenital heart disease phenotypes in the current ACMG actionable gene list, this is likely to evolve over time.† Emerging evidence suggests that BrS may be reclassified as a cardiomyopathy.Sources of incidental variants include the use of ES or GS not only for clinical testing in clinical care, such as with undiagnosed syndromes and critically ill children, but also with direct-to-consumer genetic tests and individuals participating in research studies such as population biobanks. Furthermore, some health systems have implemented genomic medicine programs incorporating population-based genetic risk testing. These testing methods can include CVD genes interrogated by chance, without a valid clinical indication, or in the absence of disease, among others. The intent of action is thus preventive, that is, precision health, rather than management of established disease, that is, precision medicine, although unrecognized genetic CVD can sometimes be diagnosed. The ACMG recommends that only LP/P variants in ACMG-78 genes be communicated to the patient if the individual has not specifically opted out of this process. Patients typically are not informed of variants designated as a variant of uncertain significance (VUS) or benign. Previously, ES and GS were often not performed in a Clinical Laboratory Improvement Amendments–approved laboratory; thus, identified variants required confirmatory testing before the results could be communicated, which has made the communication of incidental variants challenging to implement. With the advent of Clinical Laboratory Improvement Amendments–approved ES and GS, confirmatory testing may not be necessary unless there are doubts about quality. Despite this guidance for reporting, there are no recommendations on the specifics of downstream clinical evaluation, leaving researchers, testing laboratories, and clinicians who referred these patients having to make difficult decisions without clear evidence-based or expert guidelines. Last, individual- and variant-specific evaluation is best conducted at a specialized multidisciplinary CVD center, which could impose a barrier to care.Multifaceted Approach to Variant ReportingPretest/Posttest Genetic Counseling for Individuals Undergoing ES and GSPretest genetic counseling and informed consent are imperative to the process of broad-scale GS because variants outside of the specific genes of interest for the patient's clinical presentation could be communicated to patients and have implications for their family members. This should be done before genetic testing is performed. Recommendations on the points to be discussed with patients during this pretest informed consent process are the following and should be provided to the patients in writing: a discussion of the likelihood and type of incidental results that may be generated, the types of results that will or will not be communicated, the benefits and risks of GS and its limitations, potential implications for family members (including the potential impact of a CVD-associated variant on insurability and the financial costs associated with evaluation of a such a variant), the distinction between clinical- and research-based testing, patient-level data sharing, and recontact policies as new knowledge is gained on the clinical significance of results.9 Patients' reactions to receiving results may vary, yet having an open conversation about the possible outcomes of genetic testing is important. The possibility of identifying an incidental genetic finding that might confer disease risk and trigger an evaluation should be discussed, and patients should be asked whether they would want to receive these results.10,11 As more individuals undergo broad-scale genomic testing in both clinical and research settings, access to and scaling of pretest and posttest genetic counseling are needed, and certified genetic counselors are central to this. This counseling may be accomplished through alternative service delivery models, including telehealth, and may include digital health tools.12Interpreting Variant and Gene PathogenicityAdvancements in GS and CVD genetic testing have also posed complex challenges in variant interpretation and classification and the application of this information to clinical care.13,14 To address these challenges, a joint consensus recommendation from the ACMG/Association for Molecular Pathology including standards and guidelines for the interpretation of genetic variants was published in 2015.1 This established a scoring system for interpreting variants as LP/P (>90% chance of being disease associated) or likely benign/benign (>90% chance of being benign), with variants in between deemed VUSs. ClinVar,15 a publicly accessible curated database, was established to serve as a resource for variant-disease associations. However, even with these guidelines and resources, inconsistencies in variant interpretation and pathogenicity classification across genetic testing laboratories, clinicians, and ClinVar exist.16,17 Furthermore, reclassification of variants over time has occurred, with clinically relevant variant classification changes that affect medical management recommendations.18,19 Considerable variability also exists in the quality of evidence supporting the role of many genes as causative of their associated disease. Therefore, multiple international groups, organized through ClinGen,20 have performed evidence-based reassessments of gene validity for inherited CVD phenotypes. Although many genes have been reported to cause such conditions as long QT syndrome, Brugada syndrome, heritable cardiomyopathies, and others and are routinely included on clinical genetic testing panels, this curation of genes for clinical validity evidence has found that a much more limited group of genes have definitive or strong evidence for causing these conditions.21–26 Moreover, all the CVD-susceptibility genes residing in the current ACMG-78 gene panel are irrefutable disease-associated genes; however, every variant identified in a robust CVD gene is not necessarily a disease-associated variant. This highlights the need for continued multidisciplinary follow-up of genetic variants as these relationships evolve. Therefore, genetic cardiologists, cardiovascular genetic counselors, and geneticists will need to take a more active and consistent role in variant review to ensure that the most accurate information from genetic testing is being applied to patient care over time.Establishing a Clinical and Genetic Evaluation Framework for Communication of Incidental Variants and EvaluationThe communication of incidental findings to individuals undergoing broad sequencing affords an opportunity to identify genomic risk, to diagnose genetic conditions that may otherwise be left undiagnosed, to initiate surveillance and management, and potentially to prevent diseases or bad outcomes associated with diseases. To actualize this preventive potential, clinicians managing patients with incidental findings will need to use established clinical frameworks for comprehensive genetic and cardiovascular baseline evaluation and follow-up evaluation. The approach should include medical history; family history; physical examination; relevant diagnostic testing; including imaging; and variant evaluation and correlation with the potential phenotype(s) in question with the goal of balancing the risks of overdiagnosis and health care overuse with the benefits of preventing serious adverse clinical outcomes.27A Framework for Variant InterpretationIncidentally identified variants in CVD genes should be interpreted within a framework that integrates the likelihood that an identified variant is truly disease associated with the likelihood that the individual positive for the variant has the disease associated with the variant in question (Figure 1). This establishes a probability of disease association that drives the scope and duration of follow-up and, if evidence of disease is identified, downstream management. Often, this framework is a re-evaluation of an already identified incidental variant and is best accomplished in a center with expertise in cardiovascular genetics. A framework for variant interpretation that reflects this probabilistic nature uses a Bayesian approach, which is commonly used in genetic risk assessment. In a Bayesian framework, an incidentally identified variant is assessed for likelihood of disease pathogenicity in a given individual on the basis of (1) a pretest probability of disease, defined by the likelihood that the person hosting the variant has the disease associated with the variant, and (2) modification of this pretest probability by the strength of association of the genetic variant with disease, defined by how likely it is that a specific variant may cause the disease in question, to arrive at (3) a posttest probability that the variant is truly disease associated, which determines downstream management and follow-up. Given the heterogeneity of practice in a rapidly evolving field, the major goal of this scientific statement is to establish an expert-based consensus framework. Specific details around each step of this framework are delineated in the following sections.Download figureDownload PowerPointFigure 1. A framework for the evaluation of incidentally identified variants found in CVD-associated genes. In partnership with a specialized inherited cardiovascular disease (CVD) center, individuals found to have an incidentally identified variant should undergo a comprehensive clinical evaluation for the CVD in question. This pretest probability of having the CVD in question should be modified by the strength of the gene variant with CVD to arrive at a posttest probability that the variant in question places the patient at risk of developing disease. This determines the need for additional clinical evaluation, management, and follow-up. ACM indicates arrhythmic cardiomyopathy/arrhythmogenic right ventricular cardiomyopathy; BrS, Brugada syndrome; CPVT, catecholaminergic polymorphic ventricular tachycardia; CT, computed tomography; DCM, nonischemic dilated cardiomyopathy; HTAD, heritable thoracic aortic disease (also known as familial thoracic aortic aneurysm and dissection); HCM, hypertrophic cardiomyopathy; LDS, Loeys-Dietz syndrome; LQTS, long QT syndrome; LP/P, likely pathogenic/pathogenic; MRI, magnetic resonance imaging; RCM, restrictive cardiomyopathy; SQTS, short QT syndrome; vEDS, vascular Ehler-Danlos syndrome; and VUS, variant of uncertain significance. *CVD implicated by the incidentally identified genetic variant in question. **Can be considered on the basis of individualized patient evaluation.Pretest Probability of Disease Association: An Individualized Clinical EvaluationIdentification of an incidentally identified LP/P variant predicted to put the patient at risk of disease development (ie, excluding carriers of autosomal recessive diseases) should trigger a comprehensive clinical evaluation of the individual hosting the variant to establish the pretest probability of disease. Specifically, a comprehensive medical history, family history (at least 3 generations), physical examination, and clinical testing should be conducted by a clinician who is knowledgeable about the potentially implicated disease. Clinical testing should be individualized on the basis of the findings of this evaluation, the specific disease, and the previous clinical testing that may have been performed. Although individual practice may vary, individuals with incidental findings of genetic variants associated with cardiac ion channelopathies should typically have an ECG, minimum 24-hour Holter monitor, and exercise stress test (if able to be performed safely by the individual). Patients with an incidental variant in a cardiomyopathy-associated gene should be evaluated with an ECG and echocardiogram. Advanced imaging (ie, cardiac magnetic resonance imaging for tissue characterization) can be considered given the individual patient evaluation. Individuals with a thoracic aortic disease–associated gene should be evaluated with an echocardiogram, and advanced imaging can be considered (ie, computed tomography or magnetic resonance imaging to evaluate for thoracic aortic disease). For individuals carrying a familial hypercholesterolemia–associated variant, a serum lipid panel should be performed, as well as, if appropriate, further testing such as computed tomography coronary angiography. Last, for individuals with congenital/structural heart disease–associated incidental variants, an ECG and echocardiogram should be performed.3,4,6,14,28–31 Advanced imaging such as cardiac magnetic resonance imaging can be considered in some cases with congenital heart disease–associated variants. On the basis of findings from this initial clinical evaluation, additional testing such as advanced imaging may be needed. This evaluation should be conducted by an individual or a multidisciplinary team qualified to evaluate for the disease in question because the goal is to determine the likelihood that the individual demonstrates evidence of the disease prompted by the incidental variant.Although the ACMG recommends reporting of LP/P incidental variants, incidental VUSs may still be reported to patients through a number of mechanisms such as a patient-initiated request for expanded genetic testing findings or direct-to-consumer genetic testing. Although not all VUSs will be disease associated, some will be. The decision of whether to evaluate a VUS within this framework should be taken on a case-by-case basis and in close partnership with cardiovascular genetics experts in the context of a multidisciplinary team discussion.Modification of Pretest Probability: Re-Evaluation of Gene and Genetic Variant Association With DiseaseThe pretest probability of disease established after a comprehensive clinical evaluation should be modified by the strength of the genetic variants associated with CVD. According to ACMG guidelines, only incidentally identified variants that are LP/P should be reported; however, genetic testing laboratories assign variant pathogenicity differently, and the pathogenicity assertions can change over time. Thus, it is critical for the clinician to re-evaluate the veracity of the pathogenicity assignment for each variant identified rather than relying solely on the laboratory interpretation (Figure 2). This evaluation and determination of subsequent follow-up is best done at, or in close consultation with, a multidisciplinary center specializing in cardiovascular genetics.32 Several resources exist, and several more are in development, to provide a contemporaneous assessment of variant pathogenicity with disease, including ClinVar, ClinGen, and others.33 ACMG guidelines on the evaluation of incidentally identified variants based on fulfillment of specific criteria remain central to this process.1,2,34 Recent work has suggested that incorporation of clinical phenotype into variant interpretation may aid in the identification of disease-causative variants among some CVDs.35–37 Because the strength of phenotype influences the probability of pathogenicity, integration of clinical phenotype into variant interpretation framework may be important for re-evaluating variant association with disease. When combined, these resources can allow the expert clinician within a multidisciplinary team that specializes in genetic CVDs to reinterpret the probability that a given variant may or may not be associated with disease.Download figureDownload PowerPointFigure 2. Factors that influence the likelihood that an incidentally identified variant in a CVD-associated gene is associated with disease. Several factors (box) can increase or decrease the probability that an incidentally identified variant is associated with a cardiovascular disease (CVD). If a variant exceeds a 90% probability of being CVD associated, it is labeled likely pathogenic, whereas if a variant has >90% probability of being benign, it is labeled likely benign. Variants that do not exceed these thresholds are variants of uncertain significance (VUSs).Posttest Probability of Disease Association: Determination of Clinical Management and Follow-UpThe posttest likelihood that an incidentally identified variant is associated with disease is based on the pretesting probability that the individual hosting the variant has disease and incorporation of the strength of the evidence that the identified variant is associated with the disease into a Bayesian framework. This assessment guides subsequent clinical management and follow-up, which can be performed by, or in consultation with, the specialty center. For example, identification of an incidental variant that is found to be strongly associated with risk of HCM, even in an individual without evidence of disease, should warrant continued longitudinal follow-up (intervals as per existing HCM guidelines) for evaluation of cardiomyopathy. Conversely, an incidentally identified variant in a gene not on the ACMG list and disputed by ClinGen as to whether it is disease associated found in an individual with a reassuring clinical evaluation may prompt infrequent follow-up or no further follow-up. Any variant found to be likely disease associated (LP/P) requires longitudinal follow-up of the indi