rs876657510
Positions:
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2BP6_Very_Strong
The NM_000256.3(MYBPC3):c.1791-10_1791-8delTCCinsCCT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: not found (cov: 33)
Consequence
MYBPC3
NM_000256.3 splice_region, intron
NM_000256.3 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.55
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 11-47341252-GGA-AGG is Benign according to our data. Variant chr11-47341252-GGA-AGG is described in ClinVar as [Likely_benign]. Clinvar id is 227563.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.1791-10_1791-8delTCCinsCCT | splice_region_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.1791-10_1791-8delTCCinsCCT | splice_region_variant, intron_variant | 5 | NM_000256.3 | ENSP00000442795.1 | ||||
MYBPC3 | ENST00000399249.6 | c.1791-10_1791-8delTCCinsCCT | splice_region_variant, intron_variant | 5 | ENSP00000382193.2 | |||||
MYBPC3 | ENST00000544791.1 | n.1791-10_1791-8delTCCinsCCT | splice_region_variant, intron_variant | 5 | ENSP00000444259.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 23, 2015 | c.1791-10_1791-8delinsCCT in intron 18 of MYBPC3: This variant is not expected t o have clinical significance because this variant results in a T>C at position c .1791-10 and a C>T change at position c.1791-8 and these changes do not diverge from the splice consensus sequence and are therefore unlikely to impact splicing . - |
Cardiomyopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Dec 29, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at