The penetrance of rare variants in cardiomyopathy-associated genes: A cross-sectional approach to estimating penetrance for secondary findings

Abstract

Understanding the penetrance of pathogenic variants identified as secondary findings (SFs) is of paramount importance with the growing availability of genetic testing. We estimated penetrance through large-scale analyses of individuals referred for diagnostic sequencing for hypertrophic cardiomyopathy (HCM; 10,400 affected individuals, 1,332 variants) and dilated cardiomyopathy (DCM; 2,564 affected individuals, 663 variants), using a cross-sectional approach comparing allele frequencies against reference populations (293,226 participants from UK Biobank and gnomAD). We generated updated prevalence estimates for HCM (1:543) and DCM (1:220). In aggregate, the penetrance by late adulthood of rare, pathogenic variants (23% for HCM, 35% for DCM) and likely pathogenic variants (7% for HCM, 10% for DCM) was substantial for dominant cardiomyopathy (CM). Penetrance was significantly higher for variant subgroups annotated as loss of function or ultra-rare and for males compared to females for variants in HCM-associated genes. We estimated variant-specific penetrance for 316 recurrent variants most likely to be identified as SFs (found in 51% of HCM- and 17% of DCM-affected individuals). 49 variants were observed at least ten times (14% of affected individuals) in HCM-associated genes. Median penetrance was 14.6% (±14.4% SD). We explore estimates of penetrance by age, sex, and ancestry and simulate the impact of including future cohorts. This dataset reports penetrance of individual variants at scale and will inform the management of individuals undergoing genetic screening for SFs. While most variants had low penetrance and the costs and harms of screening are unclear, some individuals with highly penetrant variants may benefit from SFs.

Keywords: cardiomyopathy; penetrance; prevalence; secondary findings.

Graphical abstract

Figure 1

Penetrance of rare variants in aggregate by variant curation, rarity, age, and sex (A–H) In aggregate, variants curated as pathogenic and variants that are particularly rare (gnomAD allele count [AC] = 0) were most penetrant. The plot depicts aggregate estimated penetrance and 95% confidence intervals for rare variants in HCM- (A, B, C, D) and DCM-associated (E, F, G, H) genes. Variant curation was assessed following ACMG guidelines through ClinVar and CardioClassifier software with additional manual curation of variants with conflicting evidence (A and E [for HCM affected individuals: 173 P variants, 316 LP, 824 VUSs, 19 LB; for the UK Biobank: 30 P, 97 LP, 1,536 VUSs, 54 LB, 2 B; for DCM affected individuals: 21 P, 245 LP, 356 VUSs, 37 LB, 4 B; for the UK Biobank: 15 P, 505 LP, 3,933 VUSs, 108 LB, 7 B]). The variants were assessed for rarity by gnomAD AC bins, where 0 is not identified in the gnomAD dataset (B and F). Age was assessed in decades based on the cumulative proportion of affected individuals analyzed by each age timepoint (C and G). Sex was estimated with all parameters stratified by reported sex (D and H).

Figure 2

The aggregate estimates of penetrance of loss-of-function variants are high for specific genes The plot depicts estimated penetrance and 95% confidence interval of HCM-associated (A) and DCM-associated (B) rare variants. Predicted loss-of-function (pLoF) and non-pLoF variant groups are plotted in green and blue, respectively. ^∗, TTNtvs that are PSI > 90%. Pathogenic TNNT2 inframe deletions caused an increased penetrance signal for inframe deletions for both HCM and DCM (see Figure S12). PTC, premature termination codon; PAV, protein-altering variant; NMDc/NMDi, nonsense mediated decay competent/incompetent.

Figure 3

Penetrance of individual variants could be estimated for 316 recurrently observed rare variants from group 2 (A) The figure shows variant counts and subgroups for rare variants in HCM-associated (left) and DCM-associated (right) genes. (B) The pie charts plot the proportion of all variant observations in each subgroup (also denoted as “G+”). The observations approximate to the number of individuals with variants, although a small number of individuals may carry more than one variant. All, denotes frequency of the variant in affected individuals; obs, denotes observations of allele count. Group 1: variants observed recurrently in affected individuals and absent or singleton in the population; penetrance estimates are unreliable as the population frequency is uncertain. This group is expected to include most definitively pathogenic, high-penetrance variants. Group 2^∗: variants observed recurrently in affected individuals and the wider population; these are the variants most likely to be observed as secondary findings. ^∗Penetrance can be estimated. Group 3: variants observed once in affected individuals and recurrently in the population; penetrance estimates are unreliable, as the case frequency is uncertain. Variants in this group are likely either not pathogenic or have low penetrance. Group 4: variants are singleton in affected individuals and absent or singleton in the population; current data is too sparse to estimate penetrance.

Figure 4

Variant-specific estimates of penetrance for the 316 recurrently observed rare variants in CM-associated genes from group 2 An interactive widget is available for browsing the individual variants in this figure (see Figure S15). The variants depicted (HCM n = 257, A; DCM n = 59, B) were identified multiple times in affected individuals and population reference datasets and penetrance could therefore be estimated. Presented is the estimated penetrance and 95% confidence interval. The x axis denotes the number of times the variant was observed in each case cohort. AC, allele count; B/LB, benign/likely benign; VUS, variant of uncertain significance; LP, likely pathogenic; P, pathogenic.

Figure 5

Variant-specific estimates of penetrance by age can now be derived The plot depicts the age-related cumulative penetrance of five HCM-associated rare variants across age deciles from variant group 2. Presented is the estimated penetrance and 95% confidence interval. The x axis starts in the decade of the 20s as the analysis of these variants was underpowered for teens and younger. “20s” here means “by 30 years old.”

Penetrance estimates are inflated with underestimated population frequency (A) The map of the world emphasizes the large proportion of observations of MYBPC3 c.1504C>T (p.Arg502Trp) in HCM-affected individuals of Northwestern European (NWE) ancestry. The numbers on the map are the counts of rare-variant-genotype-positive observations (n ≈ cohort participants) from each cohort with the specified ancestry, and the percentages derive the proportion of observations that are due to the MYBPC3 c.1504C>T (p.Arg502Trp) variant. (B) The graph shows the estimated penetrance and 95% confidence interval for the variant on the basis of subgroups of reference dataset participants included. The penetrance is inflated when estimated with gnomAD because the variant is most common in participants with NWE ancestry (which dominates the UKBB dataset). Population frequency of gnomAD, UK Biobank, and Ensembl population genetics showed that this variant (rs375882485) is only found multiple times in NWE ancestry sub-cohorts. The map excludes Antarctica for figure clarity. A limitation is the low sample sizes for AFR, SAS, and EAS ancestries.