rs727505065
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM2BP4_StrongBP6_Very_StrongBS2
The NM_000432.4(MYL2):c.480C>T(p.Thr160=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,814 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: not found (cov: 31)
Exomes 𝑓: 0.0000034 ( 0 hom. )
Consequence
MYL2
NM_000432.4 synonymous
NM_000432.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.535
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 -14 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
?
Variant 12-110911098-G-A is Benign according to our data. Variant chr12-110911098-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 179705.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
?
High AC in GnomAdExome4 at 5 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYL2 | NM_000432.4 | c.480C>T | p.Thr160= | synonymous_variant | 7/7 | ENST00000228841.15 | |
MYL2 | NM_001406745.1 | c.438C>T | p.Thr146= | synonymous_variant | 6/6 | ||
MYL2 | NM_001406916.1 | c.423C>T | p.Thr141= | synonymous_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYL2 | ENST00000228841.15 | c.480C>T | p.Thr160= | synonymous_variant | 7/7 | 1 | NM_000432.4 | P1 | |
MYL2 | ENST00000548438.1 | c.438C>T | p.Thr146= | synonymous_variant | 6/6 | 3 | |||
MYL2 | ENST00000663220.1 | c.423C>T | p.Thr141= | synonymous_variant | 7/7 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 genomes
?
Cov.:
31
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249678Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135112
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GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461814Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 727206
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GnomAD4 genome ? Cov.: 31
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31
ClinVar
Significance: Likely benign
Submissions summary: Benign:4
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 | Apr 16, 2014 | Thr160Thr in exon 7 of MYL2: This variant is not expected to have clinical signi ficance because it does not alter an amino acid residue and is not located withi n the splice consensus sequence. - |
Hypertrophic cardiomyopathy 10 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 03, 2022 | - - |
Cardiomyopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Nov 27, 2018 | - - |
Hypertrophic cardiomyopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | All of Us Research Program, National Institutes of Health | Feb 05, 2024 | - - |
Computational scores
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Name
Calibrated prediction
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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