11-47335112-CCG-C

Position:

• chr11-47335112-CCG-C

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_000256.3(MYBPC3):​c.2833_2834delCG​(p.Arg945fs) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,459,968 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: MYBPC3 NM_000256.3 frameshift
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:6
• Conservation: PhyloP100: 2.15

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 Pathogenic. Variant got 18 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 11-47335112-CCG-C is Pathogenic according to our data. Variant chr11-47335112-CCG-C is described in ClinVar as [Pathogenic]. Clinvar id is 42660.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-47335112-CCG-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYBPC3	NM_000256.3	c.2833_2834delCG	p.Arg945fs	frameshift_variant	27/35	ENST00000545968.6	NP_000247.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYBPC3	ENST00000545968.6	c.2833_2834delCG	p.Arg945fs	frameshift_variant	27/35	5	NM_000256.3	ENSP00000442795.1
MYBPC3	ENST00000399249.6	c.2833_2834delCG	p.Arg945fs	frameshift_variant	26/34	5		ENSP00000382193.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD3 exomes AF: 0.00000405 AC: 1 AN: 246708 Hom.: 0 AF XY: 0.00000746 AC XY: 1 AN XY: 134084

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000562

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1459968 Hom.: 0 AF XY: 0.00000275 AC XY: 2 AN XY: 726224

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000506

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.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:6

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Mar 18, 2017	- -
Likely pathogenic, no assertion criteria provided	clinical testing	Stanford Center for Inherited Cardiovascular Disease, Stanford University	Jan 24, 2012	Note this variant was found in clinical genetic testing performed by one or more labs who may also submit to ClinVar. Thus any internal case data may overlap with the internal case data of other labs. The interpretation reviewed below is that of the Stanford Center for Inherited Cardiovascular Disease. MYBPC3 p.Arg945Glyfs*105 Given the type of variant, the case data, the segregation data and the absence in samples not selected for HCM (reviewed below) we consider this variant likely disease causing. The variant has been seen in at least 5 patients with cardiomyopathy, not including this patient. Anan et al (2002) reported the variant in four family members with HCM (referred to as Del. CG945). Hitomi et al (2010) found the variant in 4 of 176 HCM patients and 1 of 54 DCM patients in their Japanese cohort. This is a frame-shifting variant that creates a premature stop codon 105 codons downstream of the variant. The variant is expected to either cause a truncated protein or a completely absent protein due to nonsense-mediated mRNA decay. Many other frameshift and null variants have been identified in MYBPC3 in association with cardiomyopathy (ex. p.Trp792fs, p.Pro794fs, p.Lys1065fs, p.Cys1202fs, p.Pro1208fs, p.Trp1098ter, p.Glu1096ter, p.Cys1124ter, p.Gln1233ter). Furthermore, these types of variants in MYBPC3 are not seen in individuals without cardiomyopathy (Pan et al 2012). In total the variant has not been seen in ~64,438 published controls and individuals from publicly available population datasets. The variant was not observed in the following laboratory and published control samples: 50 individuals (Anan et al 2002), 388 (Hitomi et al 2010). The variant is not listed in the Exome Aggregation Consortium dataset (http://exac.broadinstitute.org/), which currently includes variant calls on ~64,000 individuals of European, African, Latino and Asian descent, including ~4300 East Asian individuals (matching the ancestry of our patient and most of the published cases (as of December 16th, 2014). -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jul 23, 2018	The c.2833_2834delCG variant in the MYBPC3 gene has been reported multiple times in association with familial cardiomyopathy (Anan et al., 2002; Hitomi et al., 2010). Anan et al. (2002) identified c.2833_2834delCG (reported as Del. CG945 using alternate nomenclature) in a 40 yo woman with HCM. The c.2833_2834delCG variant was also found in this patient's father, brother, and cousin, all of whom were clinically diagnosed with HCM (Anan et al., 2002). Hitomi et al. (2010) identified c.2833_2834delCG in 4 out of 176 patients with HCM and in 1 out of 54 patients with DCM. One individual with HCM and the c.2833_2834delCG pathogenic variant had an affected sibling who also harbored this variant (Hitomi et al., 2010).This pathogenic variant causes a shift in reading frame starting at codon Arginine 945, changing it to a Glycine, and creating a premature stop codon at position 105 of the new reading frame, denoted p.Arg945GlyfsX105. This variant is expected to result in either an abnormal, truncated protein product or loss of protein from this allele through nonsense-mediated mRNA decay. Other frameshift variants in the MYBPC3 gene have been reported in HGMD in association with cardiomyopathy (Stenson et al., 2014). Furthermore, the c.2833_2834delCG variant was not observed at a significant frequency in large population cohorts (Lek et al., 2016), indicating it is not a common benign variant. In summary c.2833_2834delCG in the MYBPC3 gene is interpreted as a pathogenic variant. -

Hypertrophic cardiomyopathy Pathogenic:2

Pathogenic, no assertion criteria provided	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Apr 16, 2007	- -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 17, 2022	This sequence change creates a premature translational stop signal (p.Arg945Glyfs*105) in the MYBPC3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MYBPC3 are known to be pathogenic (PMID: 19574547). For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 42660). This variant is also known as Del CG945. This premature translational stop signal has been observed in individuals with hypertrophic cardiomyopathy (PMID: 11835941, 20605413, 27532257). It has also been observed to segregate with disease in related individuals. This variant is present in population databases (rs397515987, gnomAD 0.006%). -

Hypertrophic cardiomyopathy 4 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

3billion

Jan 03, 2022

Frameshift: predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant (PVS1_VS). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000004, PM2_M). The variant has been reported at least twice as pathogenic/likely pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000042660, PMID:11835941, 3billion dataset). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs397515987; hg19: chr11-47356663;