rs878853980
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBP6_Very_Strong
The NM_000432.4(MYL2):c.42C>T(p.Asn14=) variant causes a synonymous change. The variant allele was found at a frequency of 0.0000112 in 1,613,772 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000010 ( 0 hom. )
Consequence
MYL2
NM_000432.4 synonymous
NM_000432.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.62
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 -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP6
?
Variant 12-110919155-G-A is Benign according to our data. Variant chr12-110919155-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 237783.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYL2 | NM_000432.4 | c.42C>T | p.Asn14= | synonymous_variant | 2/7 | ENST00000228841.15 | |
MYL2 | NM_001406745.1 | c.42C>T | p.Asn14= | synonymous_variant | 2/6 | ||
MYL2 | NM_001406916.1 | c.-16C>T | 5_prime_UTR_variant | 2/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYL2 | ENST00000228841.15 | c.42C>T | p.Asn14= | synonymous_variant | 2/7 | 1 | NM_000432.4 | P1 | |
MYL2 | ENST00000548438.1 | c.42C>T | p.Asn14= | synonymous_variant | 2/6 | 3 | |||
MYL2 | ENST00000546404.1 | c.42C>T | p.Asn14= | synonymous_variant | 2/2 | 2 | |||
MYL2 | ENST00000663220.1 | c.-16C>T | 5_prime_UTR_variant | 2/7 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152166Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461606Hom.: 0 Cov.: 30 AF XY: 0.00000963 AC XY: 7AN XY: 727056
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GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74344
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ClinVar
Significance: Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Hypertrophic cardiomyopathy 10 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 23, 2022 | - - |
Cardiomyopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Oct 14, 2019 | - - |
Hypertrophic cardiomyopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | All of Us Research Program, National Institutes of Health | Apr 27, 2023 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 22, 2019 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at