rs9964300
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_003803.4(MYOM1):c.192G>T(p.Ala64Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0625 in 1,612,418 control chromosomes in the GnomAD database, including 3,559 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_003803.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYOM1 | ENST00000356443.9 | c.192G>T | p.Ala64Ala | synonymous_variant | Exon 2 of 38 | 1 | NM_003803.4 | ENSP00000348821.4 | ||
MYOM1 | ENST00000261606.11 | c.192G>T | p.Ala64Ala | synonymous_variant | Exon 2 of 37 | 1 | ENSP00000261606.7 | |||
ENSG00000265399 | ENST00000580139.1 | n.198-1960C>A | intron_variant | Intron 2 of 4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0821 AC: 12485AN: 152136Hom.: 616 Cov.: 32
GnomAD3 exomes AF: 0.0631 AC: 15468AN: 245234Hom.: 598 AF XY: 0.0606 AC XY: 8085AN XY: 133446
GnomAD4 exome AF: 0.0604 AC: 88202AN: 1460164Hom.: 2938 Cov.: 33 AF XY: 0.0598 AC XY: 43400AN XY: 726252
GnomAD4 genome AF: 0.0823 AC: 12523AN: 152254Hom.: 621 Cov.: 32 AF XY: 0.0809 AC XY: 6025AN XY: 74442
ClinVar
Submissions by phenotype
not specified Benign:2
Ala64Ala in exon 2 of MYOM1: 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. It has been identified in 11.6% (473/4072) of A frican American chromosomes from a broad population by the NHLBI Exome Sequencin g Project (http://evs.gs.washington.edu/EVS; dbSNP rs9964300). -
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. -
not provided Benign:2
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Hypertrophic cardiomyopathy Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at