11-47352635-C-A

Position:

• chr11-47352635-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM5 BP4_Moderate

The NM_000256.3(MYBPC3):​c.13G>T​(p.Gly5Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000152 in 1,444,702 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G5R) has been classified as Pathogenic.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.000015 (0 hom.)
• Consequence: MYBPC3 NM_000256.3 missense
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts U:6
• Conservation: PhyloP100: 1.88

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 0 ACMG points.

• PM5: Other missense variant is known to change same aminoacid residue: Variant chr11-47352635-C-G is described in Lovd as [Pathogenic].
• BP4: Computational evidence support a benign effect (MetaRNN=0.2145879).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYBPC3	NM_000256.3	c.13G>T	p.Gly5Trp	missense_variant	1/35	ENST00000545968.6	NP_000247.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYBPC3	ENST00000545968.6	c.13G>T	p.Gly5Trp	missense_variant	1/35	5	NM_000256.3	ENSP00000442795	P4
MYBPC3	ENST00000399249.6	c.13G>T	p.Gly5Trp	missense_variant	1/34	5		ENSP00000382193	A2
MYBPC3	ENST00000544791.1	c.13G>T	p.Gly5Trp	missense_variant, NMD_transcript_variant	1/27	5		ENSP00000444259

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000431 AC: 1 AN: 231870 Hom.: 0 AF XY: 0.00000790 AC XY: 1 AN XY: 126622

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000945

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000152 AC: 22 AN: 1444702 Hom.: 0 Cov.: 30 AF XY: 0.0000167 AC XY: 12 AN XY: 718662

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: 0.0000154

Gnomad4 OTH exome AF: 0.0000838

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:6

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hypertrophic cardiomyopathy Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Mar 22, 2019	This sequence change replaces glycine with tryptophan at codon 5 of the MYBPC3 protein (p.Gly5Trp). The glycine residue is moderately conserved and there is a large physicochemical difference between glycine and tryptophan. This variant is not present in population databases (ExAC no frequency). This variant has been observed in an individual affected with hypertrophic cardiomyopathy, however this individual carried a likely pathogenic variant in a different gene (PMID: 28790153). ClinVar contains an entry for this variant (Variation ID: 217839). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: Deleterious; PolyPhen-2: Possibly Damaging; Align-GVGD: Class C1). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. 5 -
Uncertain significance, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Oct 02, 2023	This missense variant replaces glycine with tryptophan at codon 5 of the MYBPC3 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in one individual affected with hypertrophic cardiomyopathy, however, this individual carried a co-variant in a different gene with unknown clinical significance (PMID: 28790153). This variant has been identified in 1/231870 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -

Hypertrophic cardiomyopathy 4;C3715165:Left ventricular noncompaction 10 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Jul 26, 2021

- -

Cardiomyopathy Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Color Diagnostics, LLC DBA Color Health

Mar 16, 2023

This missense variant replaces glycine with tryptophan at codon 5 of the MYBPC3 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in at least one individual affected with hypertrophic cardiomyopathy (PMID: 28790153, 32841044). This variant has been identified in 1/231870 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -

Hypertrophic cardiomyopathy 4 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Molecular Genetics, Royal Melbourne Hospital

Apr 22, 2022

This sequence change is predicted to replace glycine with tryptophan at codon 5 of the MYBPC3 protein, p.(Gly5Trp). The glycine residue is weakly conserved (100 vertebrates, UCSC), and is not located in an annotated domain. There is a large physicochemical difference between glycine and tryptophan. The variant is present in a single individual in a large population cohort (rs201278114, 1/231,870 alleles, 0 homozygotes in gnomAD v2.1). The variant has been classified as a variant of uncertain significance (ClinVar ID: 217839), and has been identified in a case with hypertrophic cardiomyopathy with another variant in TNNT2 (PMID: 28790153). Multiple lines of computational evidence predict a benign effect for the missense substitution (4/5 algorithms). Based on the classification scheme RMH ACMG Guidelines v1.2.1, this variant is classified as a VARIANT OF UNCERTAIN SIGNIFICANCE. Following criteria are met: PM2. -

Hypertrophic cardiomyopathy 1 Uncertain:1

Uncertain significance, criteria provided, single submitter

research

Agnes Ginges Centre for Molecular Cardiology, Centenary Institute

Jul 03, 2015

This MYBPC3 Gly5Trp variant has not previously been reported in the general population or the literature. We have identified this variant in 1 HCM proband who also carries a second variant of uncertain significance in TNNT2 (Arg293Cys). This patient was diagnosed at 62 years and has a maximal wall thickness of 20mm. This variant is not present in the Exome Aggregation Consortium dataset (http://exac.broadinstitute.org/). Computational analyses (Polyphen2, CADD, SIFT, Grantham) support a potentially deleterious effect. More evidence and additional data is needed to confirm the role of this variant. Thus, we classify this variant as of "uncertain significance". -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.46
CardioboostCm	Benign	0.0068
BayesDel_addAF	Benign	-0.0039	T
BayesDel_noAF	Benign	-0.24
CADD	Benign	21
DANN	Uncertain	0.99
DEOGEN2	Benign	0.22	T;T;T
Eigen	Benign	-0.027
Eigen_PC	Benign	0.0031
FATHMM_MKL	Benign	0.72	D
LIST_S2	Uncertain	0.90	D;D;D
M_CAP	Benign	0.085	D
MetaRNN	Benign	0.21	T;T;T
MetaSVM	Benign	-0.83	T
MutationAssessor	Benign	1.8	L;.;.
MutationTaster	Benign	0.97	D;D;D
PrimateAI	Uncertain	0.55	T
PROVEAN	Benign	-1.4	N;N;N
REVEL	Benign	0.080
Sift	Uncertain	0.029	D;D;D
Sift4G	Uncertain	0.026	D;D;D
Polyphen		0.88	P;.;.
Vest4		0.38
MutPred		0.36		Gain of catalytic residue at G5 (P = 0.0055);Gain of catalytic residue at G5 (P = 0.0055);Gain of catalytic residue at G5 (P = 0.0055);
MVP		0.74
MPC		0.64
ClinPred		0.93	D
GERP RS		4.5
Varity_R		0.20
gMVP		0.27

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: rs201278114; hg19: chr11-47374186;