rs200710899
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_003803.4(MYOM1):c.3412C>T(p.Arg1138Cys) variant causes a missense change. The variant allele was found at a frequency of 0.000295 in 1,612,988 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 (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1138H) has been classified as Uncertain significance.
Frequency
Consequence
NM_003803.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYOM1 | NM_003803.4 | c.3412C>T | p.Arg1138Cys | missense_variant | 22/38 | ENST00000356443.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYOM1 | ENST00000356443.9 | c.3412C>T | p.Arg1138Cys | missense_variant | 22/38 | 1 | NM_003803.4 | P2 | |
MYOM1 | ENST00000261606.11 | c.3124C>T | p.Arg1042Cys | missense_variant | 21/37 | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00160 AC: 244AN: 152202Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000410 AC: 102AN: 248842Hom.: 0 AF XY: 0.000333 AC XY: 45AN XY: 135014
GnomAD4 exome AF: 0.000157 AC: 229AN: 1460668Hom.: 0 Cov.: 30 AF XY: 0.000132 AC XY: 96AN XY: 726628
GnomAD4 genome ? AF: 0.00162 AC: 247AN: 152320Hom.: 0 Cov.: 33 AF XY: 0.00158 AC XY: 118AN XY: 74474
ClinVar
Submissions by phenotype
MYOM1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 30, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Hypertrophic cardiomyopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at