Submissions for variant NM_000256.3(MYBPC3):c.821+3G>T

dbSNP: rs727503213

Total submissions: 9

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000768509	SCV000271998	likely pathogenic	Hypertrophic cardiomyopathy	2022-04-05	criteria provided, single submitter	clinical testing	The p.821+3G>T variant in MYBPC3 has been reported in 4 individuals with hypertrophic cardiomyopathy (HCM) and segregated with disease in 3 affected individuals from 3 families (Kassem 2013 PMID: 23233322, Singer 2019 PMID: 30645170, Robyns 2020 PMID: 31513939, LMM data). This variant has also been reported by other clinical laboratories in ClinVar (Variation ID 228869) and was absent from large population studies. This variant is located in the 5' splice region. Computational tools predict a splicing impact, which is corroborated by in vitro functional studies on patient RNA from both blood and cardiac myocardium that show that this variant results in the skipping of exon 7 (Singer 2019 PMID: 30645170). Loss of exon 7 is predicted to result in a frameshift and a subsequent premature termination codon. In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely pathogenic for autosomal dominant HCM. ACMG/AMP Criteria applied: PS4_Supporting, PM2_Supporting, PS3_Moderate, PP1, PP3.
Labcorp Genetics (formerly Invitae), Labcorp	RCV000768509	SCV001236912	pathogenic	Hypertrophic cardiomyopathy	2024-07-30	criteria provided, single submitter	clinical testing	This sequence change falls in intron 7 of the MYBPC3 gene. It does not directly change the encoded amino acid sequence of the MYBPC3 protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or altered protein product. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individuals with hypertrophic cardiomyopathy (PMID: 23233322, 30645170, 31513939). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 228869). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of exon 7, and produces a non-functional protein and/or introduces a premature termination codon (PMID: 30645170). For these reasons, this variant has been classified as Pathogenic.
Agnes Ginges Centre for Molecular Cardiology, Centenary Institute	RCV004786569	SCV001245071	likely pathogenic	Hypertrophic cardiomyopathy 4	2019-08-22	criteria provided, single submitter	research	MYBPC3 c.821+3G>T variant has been reported in one HCM case, this proband carried another MYBPC3 variant however, only the c.821+3G>T variant segregated to another affected family member (Kassem HSh, et al., 2013). The variant is absent from the Genome Aggregation Database (http://gnomad.broadinstitute.org/). In silico tools MaxEntScan and AdaBoost predict that this variant is likely to cause aberrant splicing. We identified this heterozygous variant in a Lebanese child born into a consanguineous family who was diagnosed with severe HCM. Amplification of RNA extracted from septal myectomy tissue and blood showed skipping of exon 7 in MYBPC3 (Singer et al., 2019). Loss of exon 7 is predicted to result in a shift in the reading frame and a subsequent premature stop codon . Based on the adapted ACMG criteria (Kelly MA, et al., 2018) this variant is very rare in the general population (PM2), in silico tools predict aberrant splicing to occur and this was confirmed in RNA studies which showed exon 7 skipping (PS3), and the variant has been reported in a total of 2 unrelated HCM probands (PS4_supporting), therefore we classify MYBPC3 c.821+3G>T as 'likely pathogenic'.
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	RCV001170206	SCV001332758	likely pathogenic	Cardiomyopathy	2017-11-09	criteria provided, single submitter	clinical testing
GeneDx	RCV001556272	SCV001777820	likely pathogenic	not provided	2024-07-02	criteria provided, single submitter	clinical testing	Published functional studies suggest skipping of exon 7 (PMID: 30645170); Not observed in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 31513939, 23233322, 30645170, 36243179, 36252119, 36264615)
Ambry Genetics	RCV002427004	SCV002678283	likely pathogenic	Cardiovascular phenotype	2024-09-10	criteria provided, single submitter	clinical testing	The c.821+3G>T intronic variant results from a G to T substitution 3 nucleotides after coding exon 7 in the MYBPC3 gene. This variant has been reported in multiple individuals with hypertrophic cardiomyopathy (HCM) and has been shown to segregate with disease in two affected relatives (Kassem HSh et al. J Cardiovasc Transl Res, 2013 Feb;6:65-80; Singer ES et al. Circ Genom Precis Med, 2019 01;12:e002368; Robyns T et al. Eur J Med Genet, 2020 Mar;63:103754; Ambry internal data). This nucleotide position is not well conserved in available vertebrate species. However, in silico splice site analysis predicts that this alteration will weaken the native splice donor site, and RNA studies have demonstrated exon 7 skipping in heterozygous individuals (Singer ES et al. Circ Genom Precis Med, 2019 01;12:e002368). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the majority of available evidence to date, this variant is likely to be pathogenic.
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	RCV004786569	SCV005398404	pathogenic	Hypertrophic cardiomyopathy 4	2023-07-16	criteria provided, single submitter	clinical testing	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with dilated cardiomyopathy 1MM (MIM#615396), hypertrophic cardiomyopathy 4 (MIM#115197) and left ventricular noncompaction 10 (MIM#615396) (OMIM). (I) 0108 - This gene is associated with both recessive and dominant disease. Heterozygous variants are frequently reported in adult onset conditions, however recessive inheritance results in a more severe early onset phenotype (OMIM). (I) 0210 - Splice site variant proven to affect splicing of the transcript with a known effect on protein sequence. Analysis of RNA from individuals heterozygous for this variant have demonstrated the out-of-frame skipping of exon 7, resulting in a premature termination codon (p.(Glu258Glyfs*26)) which is predicted to undergo NMD (PMID: 30645170). (SP) 0115 - Variants in this gene are known to have variable expressivity (PMID: 32841044). (I) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0311 - An alternative nucleotide change at the same canonical splice site, is present in gnomAD (v3) (1 heterozygote, 0 homozygotes). (I) 0701 - Other null variants comparable to the one identified in this case have very strong previous evidence for pathogenicity. Other NMD-predicted variants have been classfied as likely pathogenic and pathogenic by multiple clinical diagnostic laboratories (DECIPHER). It should also be noted that alternate splice site variants affecting the same nucleotide position (c.821+3G>A, c.821+3G>C) have been reported as VUS favouring pathogenicity, and observed in an individual with HCM (ClinVar, PMID: 26656175). (SP) 0808 - Previous reports of pathogenicity for this variant are conflicting. This variant has been reported in at least seven unrelated individuals (including two families) with HCM and has been classified as either a VUS, likely pathogenic or pathogenic (ClinVar, LOVD, PMIDs: 23233322, 31513939, 30645170). (I) 0905 - No published segregation evidence has been identified for this variant. (I) 1007 - No published functional evidence has been identified for this variant. (I) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign
Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute	RCV002427004	SCV006068374	likely pathogenic	Cardiovascular phenotype	2022-12-07	criteria provided, single submitter	clinical testing
Center for Human Genetics, University of Leuven	RCV000768509	SCV000886816	uncertain significance	Hypertrophic cardiomyopathy	2018-10-31	flagged submission	clinical testing