ClinVar Genomic variation as it relates to human health

This sequence change falls in the splice region of the acceptor site of intron 5 of FLNC. The variant is present in a large population cohort at a frequency of 0.005% (rs532143625, 15/280,590 alleles, 0 homozygotes in gnomAD v2.1). It has been classified as a variant of uncertain significance and pathogenic previously (ClinVar, LOVD). The variant has been identified in at least two probands with dilated cardiomyopathy (PMID: 32112656, Shariant), and compound heterozygous with a second pathogenic allele in an individual with cardiomyopathy (https://doi.org/10.1161/res.127.suppl_1.454). The nucleotide is not conserved (100 vertebrates, UCSC), and multiple lines of computational evidence predict a impact on splicing (SpliceAI, MaxEntScan, NNSplice). Based on the classification scheme RMH Modified ACMG Guidelines v1.3.1, this variant is classified as a VARIANT OF UNCERTAIN SIGNIFICANCE . Following criteria are met: PP3.

Truncating variants in FLNC are reported to cause a highly penetrant form of arrhythmogenic cardiomyopathy (Gigli, Circulation, 2021). The FLNC c.970-4A>G variant was identified in 4 probands with arrhythmogenic cardiomyopathy, and the variant cosegregated with phenotype in heterozygous family members. Computational tools predicted that the variant activated a cryptic splice acceptor site 3 nucleotides adjacent to the canonical site, leading to inclusion of an in-frame premature termination codon in the mature mRNA. Functional studies confirmed this molecular event in peripheral blood and iPSC-CM RNA analyses, provoking a phenotype consistent with other truncating FLNC variants. These data collectively support criteria to classify FLNC c.970-4A>G as pathogenic.

This sequence change falls in intron 5 of the FLNC gene. It does not directly change the encoded amino acid sequence of the FLNC protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. This variant is present in population databases (rs532143625, gnomAD 0.009%). This variant has been observed in individuals with clinical features of FLNC-related conditions (PMID: 32112656, 34587765, 37164047; Invitae). ClinVar contains an entry for this variant (Variation ID: 432231). Studies have shown that this variant results in activation of a cryptic splice site and introduces a premature termination codon (PMID: 37164047). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic.

The c.970-4A>G intronic variant results from an A to G substitution 4 nucleotides before coding exon 6 in the FLNC gene. This variant has been detected in probands with dilated cardiomyopathy (DCM) and/or arrhythmogenic cardiomyopathy, and has shown some segregation with disease features in families; however, in some cases, clinical details were limited or additional variants in cardiac-related genes were detected (Verdonschot JAJ et al. Hum Mutat, 2020 06;41:1091-1111; Gigli M et al. Circulation. 2021 Nov;144(20):1600-1611; O'Neill MJ et al. Heart Rhythm. 2023 Aug;20(8):1158-1166). RNA studies by one group have indicated that this alteration results in abnormal splicing (O'Neill MJ et al. Heart Rhythm. 2023 Aug;20(8):1158-1166). This nucleotide position is not well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will result in the creation or strengthening of a novel splice acceptor site. Based on the available evidence, the clinical significance of this alteration remains unclear.

Identified in patients with cardiomyopathy, including DCM and ACM in published literature; several patients harbored additional cardiogenetic variants (PMID: 32112656, 34587765, 37164047); Identified in an abstract by Ohiri, 2020 in trans with a nonsense variant in the FLNC gene in a patient with postpartum cardiomyopathy and skeletal muscle disease; A published functional study demonstrates a damaging effect as c.970-4A>G activated the cryptic SAS, introducing a 3-bp insertion which results in protein truncation and nonsense mediated decay; patch clamp studies also showed irregular spontaneous action potentials, increased action potential duration, and increased sodium late current (PMID: 37164047); In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 32112656, 37164047, 34587765)

The FLNC c.970-4A>G variant is predicted to interfere with splicing. This variant has been reported in an individual with dilated cardiomyopathy (Verdonschot et al. 2020. PubMed ID: 32112656, table 1) and in an additional large cohort study of patients with FLNC truncating variants and varied cardiac phenotypes (Gigli et al. 2021. PubMed ID: 34587765). An outside laboratory indicated this variant was detected in 4 probands with segregation in affected family members; however, additional details were not provided (https://www.ncbi.nlm.nih.gov/clinvar/variation/432231/). This variant is reported in 0.010% of alleles in individuals of European (non-Finnish) descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.