rs397515893

Positions:

• chr11-47343158-C-T

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PP3_Moderate PP5_Very_Strong

The NM_000256.3(MYBPC3):​c.1227-13G>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000871 in 1,607,902 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 Likely pathogenic (★★).

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0000089 (0 hom.)
• Consequence: MYBPC3 NM_000256.3 splice_polypyrimidine_tract, intron
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:13 U:1
• Conservation: PhyloP100: -0.0880

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 10 ACMG points.

• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 11-47343158-C-T is Pathogenic according to our data. Variant chr11-47343158-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 42513.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYBPC3	NM_000256.3	c.1227-13G>A		splice_polypyrimidine_tract_variant, intron_variant		ENST00000545968.6	NP_000247.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYBPC3	ENST00000545968.6	c.1227-13G>A		splice_polypyrimidine_tract_variant, intron_variant		5	NM_000256.3	ENSP00000442795	P4
MYBPC3	ENST00000399249.6	c.1227-13G>A		splice_polypyrimidine_tract_variant, intron_variant		5		ENSP00000382193	A2
MYBPC3	ENST00000544791.1	c.1227-13G>A		splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant		5		ENSP00000444259

Frequencies

GnomAD3 genomes AF: 0.00000657 AC: 1 AN: 152212 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0000942

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000125 AC: 3 AN: 239054 Hom.: 0 AF XY: 0.0000154 AC XY: 2 AN XY: 129902

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000298

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.0000490

Gnomad NFE exome AF: 0.00000924

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000893 AC: 13 AN: 1455690 Hom.: 0 Cov.: 31 AF XY: 0.00000829 AC XY: 6 AN XY: 723384

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: 0.0000117

Gnomad4 FIN exome AF: 0.0000191

Gnomad4 NFE exome AF: 0.00000992

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00000657 AC: 1 AN: 152212 Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1 AN XY: 74352

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.0000942

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000207 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:13 Uncertain:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hypertrophic cardiomyopathy Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Feb 01, 2019	The c.1227-13G>A variant in MYBPC3 has been reported in 5 individuals with hypertrophic cardiomyopathy (HCM) and segregated with disease in 3 affected individuals from 2 families (Jaaskelainen 2002, Mendes de Almeida 2017, Núñez 2013, LMM data). It has also been identified in 2/23872 Finnish chromosomes by gnomAD (http://gnomad.broadinstitute.org) and has been reported in ClinVar (Variation ID: 42513). This variant is located in the 3' splice region. RNA analysis from peripheral blood obtained from an affected individual showed that this variant introduces a cryptic splice site leading to an insertion of 11 intronic nucleotides and subsequently a frameshift and premature termination 16 amino acids downstream (Jaaskelainen 2002). This alteration is then predicted to lead to a truncated or absent protein. Loss of function of the MYBPC3 gene is an established disease mechanism in autosomal dominant HCM. In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant HCM. ACMG/AMP Criteria applied: PVS1, PM2_Supporting, PP1, PP3, PS4_Supporting. -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 09, 2024	This sequence change falls in intron 14 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 disrupted protein product. This variant is present in population databases (rs397515893, gnomAD 0.004%). This variant has been observed in individuals with hypertrophic cardiomyopathy (PMID: 12110947, 23782526, 28797094; Invitae). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 42513). Studies have shown that this variant results in use of a cryptic splice site and introduces a premature termination codon (PMID: 12110947). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Genetics and Molecular Pathology, SA Pathology	Jan 17, 2023	The MYBPC3 c.1227-13G>A variant is classified as Pathogenic (PS4, PP1_Strong, PS3_Moderate, PM2) MYBPC3 c.1227-13G>A is located in intron 14/34 and is expected to create a strong cryptic splice site downstream of the canonical splice site. Functional studies confirm insertion of an 11bp fragment resulting in an aberrant protein with a shift in the reading frame and premature termination (PMID#12110947) (PS3_moderate). This is supported by multiple in-silico tools (PMID#28679633). This variant has been reported in at least 15 probands with a clinical presentation of Hypertrophic cardiomyopathy (12110947, 32451163, 28679633, 30775854, 28797094, 22857948, 23782526) (PS4) and is reported to co-segregate with disease in 7 affected family members in 2 families (PMID##12110947 and 32451163) (PP1_strong). The variant is reported in dbSNP (rs397515893), reported as disease causing in the HGMD database (CS21760), reported as pathogenic/likely pathogenic by other diagnostic laboratories (ClinVar#42513) and is rare in population databases (gnomAD allele frequency = 0.00065%; 1 het) (PM2). -
Pathogenic, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Nov 09, 2023	The c.1227-13G>A variant of the MYBPC3 gene has been observed in multiple individuals with hypertrophic cardiomyopathy (PMID: 12110947, 22857948, 23782526, 22267749, 32451163, 33673806). It has also been observed to segregate with disease in related individuals (PMID: 12110947, 32451163). RNA analysis from peripheral blood obtained from an affected individual showed that this variant introduces a cryptic splice site leading to an insertion of 11 intronic nucleotides and subsequently a frameshift and premature termination codon (PMID: 12110947). The resulting mRNA is expected to undergo nonsense-mediated decay. Loss-of-function variants in MYBPC3 are known to be pathogenic (PMID: 19574547). Based on these evidence, the c.1227-13G>A variant in MYBPC3 is classified as pathogenic. -

Hypertrophic cardiomyopathy 4 Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	3billion	Feb 23, 2023	The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.001%). This variant was previously reported to alter splicing and result in a loss of normal protein fucnction through nonsense-mediated decay (NMD) or protein truncation (ClinVar ID: RCV000009137). The variant has been reported to co-segregate with the disease in at least 7 similarly affected relatives/individuals in at least two unrelated families (PMID: 12110947, 23782526, 25611685, 28797094). The variant has been reported at least twice as pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000042513). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline. -
Pathogenic, criteria provided, single submitter	clinical testing	Molecular Genetics, Royal Melbourne Hospital	Nov 05, 2023	This sequence change in MYBPC3 is an intronic variant located in intron 14. The highest population minor allele frequency in the population database gnomAD v2.1 is 0.007% (2/23,872 alleles) in the Finnish population, while the highest non-founder population minor allele frequency is 0.003% (1/34,354 alleles) in the Latino/Admixed American population which is consistent with hypertrophic cardiomyopathy. This variant has been reported in multiple unrelated individuals with hypertrophic cardiomyopathy and segregates with disease in at least two families (PMID: 12110947, 25611685, 32451163, 33673806). The results from an in silico splicing predictor (SpliceAI) indicate that this variant may impact splicing by disrupting the acceptor splice site of intron 14 of MYBPC3. This prediction is confirmed by splicing assays demonstrating that the variant impacts splicing by activating an acceptor site leading to an 11 bp insertion of intron 14 that is expected to undergo nonense-mediated decay (PMID: 12110947, 28679633). Based on the classification scheme RMH Modified ACMG/AMP Guidelines v1.6.1, this variant is classified as PATHOGENIC. Following criteria are met: PVS1, PS4, PP1_Moderate, PM2_Supporting. -
Pathogenic, criteria provided, single submitter	clinical testing	Mendelics	May 04, 2022	- -

Cardiomyopathy Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	Apr 21, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Aug 08, 2023	This variant causes a G to A nucleotide substitution at the -13 position of intron 14 of the MYBPC3 gene. A functional study using RNA derived from a carrier individual carrier has shown that this variant results in aberrant splicing, inserting 11 nucleotides, and is predicted to create a frameshift and premature translation stop signal (PMID: 12110947). This variant has been reported in at least 15 individuals affected with hypertrophic cardiomyopathy (PMID: 12110947, 22267749, 22857948, 24888384, 32163302, 32451163, 33673806, 35508642, 37178278). It has been shown that this variant segregates with disease in 8 affected relatives from 3 families (PMID: 12110947, 22267749, 32451163). This variant has been identified in 4/270442 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of MYBPC3 function is a known mechanism of disease (clincalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Blueprint Genetics	Dec 18, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jan 26, 2024	Not observed at significant frequency in large population cohorts (gnomAD); Published cDNA analysis performed from RNA of a patient with this variant demonstrated a damaging effect through creation of a new cryptic splice acceptor site upstream of the natural site, which results in insertion of intronic sequence, frameshift, and introduction of a premature stop codon (PMID: 12110947); In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 25228707, 26936621, 28797094, 23782526, 22267749, 24704860, 24888384, 30775854, 32163302, 12110947, 33673806, 22857948, 32451163, 18273486, 25611685, 34461741, 28679633) -

Primary familial hypertrophic cardiomyopathy Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

May 16, 2021

Variant summary: MYBPC3 c.1227-13G>A alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes the canonical 3' acceptor site. Four predict the variant creates a new 3' acceptor site eleven nucleotides upstream of the canonical 3' splice acceptor site. At least one publication reports experimental evidence that this variant affects mRNA splicing by inserting eleven intronic nucleotides following the cryptic splice site between exons 14 and 15 (Jaaskelainen_2002). The variant allele was found at a frequency of 1.2e-05 in 240844 control chromosomes. c.1227-13G>A has been reported in the literature in multiple individuals affected with Hypertrophic Cardiomyopathy and co-segregated with disease in multiple pedigrees (example, Brito_2012, Fokstuen_2014, Nunez_2013, Page_2012, Jaaskelainen_2002, Mendes de Almeida_2017, Gomes_2020). These data indicate that the variant is very likely to be associated with disease. Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation (Pathogenic, n=3; VUS, n=1). Based on the evidence outlined above, the variant was classified as pathogenic. -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Jan 11, 2023

The c.1227-13G>A intronic pathogenic mutation results from a G to A substitution 13 nucleotides upstream from coding exon 15 in the MYBPC3 gene. This nucleotide position is not well conserved in available vertebrate species. This variant has been detected in multiple individuals with hypertrophic cardiomyopathy (HCM) (Brito D et al. Rev Port Cardiol, 2012 Sep;31:577-87; Núñez L et al. Circ. J., 2013 Jun;77:2358-65; Page SP et al. Circ Cardiovasc Genet, 2012 Apr;5:156-66; Captur G et al. Circ Cardiovasc Genet, 2014 Jun;7:241-8; Hathaway J et al. BMC Cardiovasc Disord, 2021 Mar;21:126) This alteration has also been shown to co-segregate with HCM in families (Jääskeläinen P et al. J. Mol. Med., 2002 Jul;80:412-22; Mendes de Almeida R et al. PLoS ONE, 2017 Aug;12:e0182946; Gomes AC et al. Rev Port Cardiol (Engl Ed), 2020 Apr;39:227.e1-227.e9). In silico splice site analysis predicts that this alteration may weaken the native splice acceptor site and will result in the creation or strengthening of a novel splice acceptor site. In one study, cDNA analysis reportedly showed use of an upstream cryptic acceptor splice site, causing a translational frameshift with a predicted alternate stop codon (Jääskeläinen P et al. J. Mol. Med., 2002 Jul;80:412-22). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

not specified Uncertain:1

Uncertain significance, flagged submission

clinical testing

Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute

Jun 08, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	22
DANN	Benign	0.71

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.98		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.98		Position offset: -2
DS_AL_spliceai		0.40		Position offset: -13

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

Publications

LitVar

Other links and lift over

dbSNP: rs397515893; hg19: chr11-47364709;