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NM_000256.3(MYBPC3):c.3190+4C>T

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(5)

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Jan 7, 2021)
Last evaluated:
Oct 19, 2020
Accession:
VCV000181003.7
Variation ID:
181003
Description:
single nucleotide variant
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NM_000256.3(MYBPC3):c.3190+4C>T

Allele ID
179208
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11p11.2
Genomic location
11: 47333553 (GRCh38) GRCh38 UCSC
11: 47355104 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000011.10:g.47333553G>A
NC_000011.9:g.47355104G>A
NM_000256.3:c.3190+4C>T MANE Select
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000011.10:47333552:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (A)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00006
1000 Genomes Project 0.00020
The Genome Aggregation Database (gnomAD), exomes 0.00010
Exome Aggregation Consortium (ExAC) 0.00009
The Genome Aggregation Database (gnomAD) 0.00006
Links
ClinGen: CA013630
dbSNP: rs571457875
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Oct 19, 2020 RCV000158221.4
Uncertain significance 1 criteria provided, single submitter Aug 23, 2020 RCV000629030.3
Uncertain significance 1 criteria provided, single submitter Jun 23, 2017 RCV000766370.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Jan 24, 2019 RCV001171134.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
MYBPC3 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
2377 2392

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jun 23, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000208156.10
Submitted: (Jan 29, 2019)
Evidence details
Comment:
This varaint is denoted c.3190+4 C>T: IVS29+4 C>T in intron 29 of the MYBPC3 gene (NM_000256.3). The c.3190+4 C>T variant in the MYBPC3 gene has … (more)
Uncertain significance
(Oct 28, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000271993.2
Submitted: (Mar 21, 2019)
Evidence details
Comment:
The c.3190+4C>T variant in MYBPC3 has not been previously reported in individual s with cardiomyopathy, but has been identified in 9/16308 South Asian chromosome s … (more)
Uncertain significance
(Jul 31, 2018)
criteria provided, single submitter
Method: clinical testing
Cardiomyopathy
Allele origin: germline
CHEO Genetics Diagnostic Laboratory,Children's Hospital of Eastern Ontario
Accession: SCV001333815.1
Submitted: (Mar 03, 2020)
Evidence details
Likely benign
(Jan 24, 2019)
criteria provided, single submitter
Method: clinical testing
Cardiomyopathy
Allele origin: germline
Color Health, Inc
Accession: SCV001358824.1
Submitted: (May 19, 2020)
Evidence details
Uncertain significance
(Oct 19, 2020)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001442816.1
Submitted: (Nov 10, 2020)
Evidence details
Publications
PubMed (3)
Comment:
Variant summary: MYBPC3 c.3190+4C>T alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly … (more)
Uncertain significance
(Aug 23, 2020)
criteria provided, single submitter
Method: clinical testing
Hypertrophic cardiomyopathy
Allele origin: germline
Invitae
Accession: SCV000749940.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (5)
Comment:
This sequence change falls in intron 29 of the MYBPC3 gene. It does not directly change the encoded amino acid sequence of the MYBPC3 protein, … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Incidentally identified genetic variants in arrhythmogenic right ventricular cardiomyopathy-associated genes among children undergoing exome sequencing reflect healthy population variation. Headrick AT Molecular genetics & genomic medicine 2019 PMID: 30985088
Hypertrophic cardiomyopathy clinical phenotype is independent of gene mutation and mutation dosage. Viswanathan SK PloS one 2017 PMID: 29121657
Identification of pathogenic gene mutations in <i>LMNA</i> and <i>MYBPC3</i> that alter RNA splicing. Ito K Proceedings of the National Academy of Sciences of the United States of America 2017 PMID: 28679633
Pathogenic variant burden in the ExAC database: an empirical approach to evaluating population data for clinical variant interpretation. Kobayashi Y Genome medicine 2017 PMID: 28166811
Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. Buratti E Nucleic acids research 2007 PMID: 17576681
Statistical features of human exons and their flanking regions. Zhang MQ Human molecular genetics 1998 PMID: 9536098

Text-mined citations for rs571457875...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Jul 07, 2021