chr11-47337481-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM1PM2PP3
The NM_000256.3(MYBPC3):c.2512G>A(p.Glu838Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,606 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. E838Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_000256.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYBPC3 | NM_000256.3 | c.2512G>A | p.Glu838Lys | missense_variant | 25/35 | ENST00000545968.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYBPC3 | ENST00000545968.6 | c.2512G>A | p.Glu838Lys | missense_variant | 25/35 | 5 | NM_000256.3 | P4 | |
MYBPC3 | ENST00000399249.6 | c.2512G>A | p.Glu838Lys | missense_variant | 24/34 | 5 | A2 | ||
MYBPC3 | ENST00000544791.1 | c.*17G>A | 3_prime_UTR_variant, NMD_transcript_variant | 25/27 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461606Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727106
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Nov 20, 2012 | The Glu838Lys variant in MYBPC3 has not been reported in the literature nor prev iously identified by our laboratory. This variant has not been identified in lar ge and broad European American and African American populations by the NHLBI Exo me Sequencing Project (http://evs.gs.washington.edu/EVS/), though it remains pos sible that this variant is common in other populations. Computational analyses ( conservation, AlignGVGD, PolyPhen2, and SIFT) suggest that this variant may impa ct the protein, though this information is not predictive enough to determine pa thogenicity. In summary, additional information is needed to fully assess the cl inical significance of the Glu838Lys variant. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at