rs727503213

chr11-47347854-C-Achr11-47347854-C-Gchr11-47347854-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2 PP5 BP4

The NM_000256.3(MYBPC3):c.821+3G>T variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000708 in 1,412,096 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 7.1e-7 (0 hom.)
• Consequence: MYBPC3 NM_000256.3 splice_donor_region, intron
• Scores: Splicing: ADA: 0.9341
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:6 U:1
• Conservation: PhyloP100: 0.214

Genes affected

MYBPC3 (HGNC:7551): (myosin binding protein C3) MYBPC3 encodes the cardiac isoform of myosin-binding protein C. Myosin-binding protein C is a myosin-associated protein found in the cross-bridge-bearing zone (C region) of A bands in striated muscle. MYBPC3 is expressed exclusively in heart muscle and is a key regulator of cardiac contraction. Mutations in this gene are a frequent cause of familial hypertrophic cardiomyopathy. [provided by RefSeq, May 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 11-47347854-C-A is Pathogenic according to our data. Variant chr11-47347854-C-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 228869.We mark this variant Likely_pathogenic, oryginal submissions are: {Pathogenic=1, Likely_pathogenic=5, Uncertain_significance=1}. Variant chr11-47347854-C-A is described in Lovd as [Likely_pathogenic].
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).. Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYBPC3	NM_000256.3	c.821+3G>T		splice_donor_region_variant, intron_variant		ENST00000545968.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYBPC3	ENST00000545968.6	c.821+3G>T		splice_donor_region_variant, intron_variant		5	NM_000256.3	P4
MYBPC3	ENST00000399249.6	c.821+3G>T		splice_donor_region_variant, intron_variant		5		A2
MYBPC3	ENST00000544791.1	c.821+3G>T		splice_donor_region_variant, intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.08e-7 AC: 1 AN: 1412096 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 697762

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:6 Uncertain:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Hypertrophic cardiomyopathy Pathogenic:3 Uncertain:1

Uncertain significance, criteria provided, single submitter	clinical testing	Center for Human Genetics, University of Leuven	Oct 31, 2018	- -
Likely pathogenic, criteria provided, single submitter	research	Agnes Ginges Centre for Molecular Cardiology, Centenary Institute	Aug 22, 2019	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'. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Apr 05, 2022	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. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Oct 14, 2020	For these reasons, this variant has been classified as Pathogenic. Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant is associated with exon skipping, which introduces a frameshift (PMID: 30645170). The resulting mRNA is expected to undergo nonsense-mediated decay. This variant has been observed in individual(s) 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). This variant is not present in population databases (ExAC no frequency). 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 likely results in a truncated protein product. -

Cardiomyopathy Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario

Nov 09, 2017

- -

not provided Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Jan 25, 2021

Not observed in large population cohorts (Lek et al., 2016); In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 30645170, 23233322, 31513939) -

Cardiovascular phenotype Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Oct 25, 2021

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 variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). 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). Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
Cadd	Benign	7.3
Dann	Benign	0.70

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.93
dbscSNV1_RF	Benign	0.46
SpliceAI score (max)		0.71		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.71		Position offset: 3

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs727503213; hg19: chr11-47369405;