rs369096037
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP6_Very_Strong
The NM_000256.3(MYBPC3):c.1624+14_1624+15insA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000524 in 1,564,028 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00026 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000030 ( 0 hom. )
Consequence
MYBPC3
NM_000256.3 intron
NM_000256.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.0220
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 Benign. Variant got -8 ACMG points.
BP6
Variant 11-47342563-C-CT is Benign according to our data. Variant chr11-47342563-C-CT is described in ClinVar as [Likely_benign]. Clinvar id is 42554.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.1624+14_1624+15insA | intron_variant | ENST00000545968.6 | NP_000247.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYBPC3 | ENST00000545968.6 | c.1624+14_1624+15insA | intron_variant | 5 | NM_000256.3 | ENSP00000442795 | P4 | |||
MYBPC3 | ENST00000399249.6 | c.1624+14_1624+15insA | intron_variant | 5 | ENSP00000382193 | A2 | ||||
MYBPC3 | ENST00000544791.1 | c.1624+14_1624+15insA | intron_variant, NMD_transcript_variant | 5 | ENSP00000444259 |
Frequencies
GnomAD3 genomes AF: 0.000250 AC: 38AN: 152182Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000739 AC: 15AN: 203114Hom.: 0 AF XY: 0.0000920 AC XY: 10AN XY: 108730
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GnomAD4 exome AF: 0.0000298 AC: 42AN: 1411728Hom.: 0 Cov.: 31 AF XY: 0.0000273 AC XY: 19AN XY: 696560
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GnomAD4 genome AF: 0.000263 AC: 40AN: 152300Hom.: 0 Cov.: 33 AF XY: 0.000282 AC XY: 21AN XY: 74472
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
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 03, 2017 | c.1624+14_1624+15insA in intron 17 of MYBPC3: This variant is not expected to ha ve clinical significance because it is not located within the splice consensus s equence. It has been identified in 8/57238 African chromosomes by the Exome Aggr egation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs369096037). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 27, 2018 | - - |
Hypertrophic cardiomyopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 24, 2023 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at