rs139794370
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_000432.4(MYL2):c.36C>T(p.Gly12=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000136 in 1,613,678 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. G12G) has been classified as Likely benign.
Frequency
Consequence
NM_000432.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYL2 | NM_000432.4 | c.36C>T | p.Gly12= | synonymous_variant | 2/7 | ENST00000228841.15 | |
MYL2 | NM_001406745.1 | c.36C>T | p.Gly12= | synonymous_variant | 2/6 | ||
MYL2 | NM_001406916.1 | c.-22C>T | 5_prime_UTR_variant | 2/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYL2 | ENST00000228841.15 | c.36C>T | p.Gly12= | synonymous_variant | 2/7 | 1 | NM_000432.4 | P1 | |
MYL2 | ENST00000548438.1 | c.36C>T | p.Gly12= | synonymous_variant | 2/6 | 3 | |||
MYL2 | ENST00000546404.1 | c.36C>T | p.Gly12= | synonymous_variant | 2/2 | 2 | |||
MYL2 | ENST00000663220.1 | c.-22C>T | 5_prime_UTR_variant | 2/7 |
Frequencies
GnomAD3 genomes AF: 0.000717 AC: 109AN: 152070Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000147 AC: 37AN: 251416Hom.: 0 AF XY: 0.000110 AC XY: 15AN XY: 135884
GnomAD4 exome AF: 0.0000759 AC: 111AN: 1461490Hom.: 0 Cov.: 30 AF XY: 0.0000564 AC XY: 41AN XY: 727000
GnomAD4 genome AF: 0.000716 AC: 109AN: 152188Hom.: 1 Cov.: 32 AF XY: 0.000753 AC XY: 56AN XY: 74406
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Aug 24, 2020 | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Aug 22, 2013 | Gly12Gly in exon 2 of MYL2: This variant is not expected to have clinical signif icance because it does not alter an amino acid residue and is not located within the splice consensus sequence. It has been identified in 0.1% (5/4406) of Afric an American chromosomes from a broad population by the NHLBI Exome Sequencing Pr oject (http://evs.gs.washington.edu/EVS/; dbSNP rs139794370). Gly12Gly in exon 2 of MYL2 (rs139794370; allele frequency = 0.1%, 5/4406) ** - |
not provided Benign:3
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 09, 2020 | - - |
Likely benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Cardiomyopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Nov 25, 2018 | - - |
Hypertrophic cardiomyopathy 10 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 01, 2017 | 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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at