chr12-110913382-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000432.4(MYL2):c.275-58G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0764 in 1,586,164 control chromosomes in the GnomAD database, including 5,504 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).
Frequency
Genomes: 𝑓 0.072 ( 497 hom., cov: 33)
Exomes 𝑓: 0.077 ( 5007 hom. )
Consequence
MYL2
NM_000432.4 intron
NM_000432.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0630
Genes affected
MYL2 (HGNC:7583): (myosin light chain 2) This gene encodes a major sarcomeric protein in mammalian striated muscle. The encoded protein plays a role in embryonic heart muscle structure and function, while phosphorylation of the encoded protein is involved in cardiac myosin cycling kinetics, torsion and function in adults. Mutations in this gene are associated with hypertrophic cardiomyopathy 10 and infant-onset myopathy. [provided by RefSeq, May 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYL2 | NM_000432.4 | c.275-58G>A | intron_variant | ENST00000228841.15 | NP_000423.2 | |||
MYL2 | NM_001406745.1 | c.233-58G>A | intron_variant | NP_001393674.1 | ||||
MYL2 | NM_001406916.1 | c.218-58G>A | intron_variant | NP_001393845.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYL2 | ENST00000228841.15 | c.275-58G>A | intron_variant | 1 | NM_000432.4 | ENSP00000228841.8 | ||||
MYL2 | ENST00000548438.1 | c.233-58G>A | intron_variant | 3 | ENSP00000447154.1 | |||||
MYL2 | ENST00000663220.1 | c.218-58G>A | intron_variant | ENSP00000499568.1 | ||||||
MYL2 | ENST00000549029.1 | n.106-58G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0725 AC: 11032AN: 152106Hom.: 498 Cov.: 33
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GnomAD4 exome AF: 0.0769 AC: 110203AN: 1433940Hom.: 5007 AF XY: 0.0789 AC XY: 56404AN XY: 714928
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GnomAD4 genome AF: 0.0725 AC: 11033AN: 152224Hom.: 497 Cov.: 33 AF XY: 0.0748 AC XY: 5564AN XY: 74412
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ClinVar
Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link
Submissions by phenotype
not provided Other:1
not provided, no classification provided | literature only | Leiden Muscular Dystrophy (MYL2) | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at