chr18-3067417-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_003803.4(MYOM1):c.4903G>A(p.Gly1635Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000873 in 1,613,598 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. G1635G) has been classified as Likely benign.
Frequency
Consequence
NM_003803.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYOM1 | NM_003803.4 | c.4903G>A | p.Gly1635Ser | missense_variant | 38/38 | ENST00000356443.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYOM1 | ENST00000356443.9 | c.4903G>A | p.Gly1635Ser | missense_variant | 38/38 | 1 | NM_003803.4 | P2 | |
MYOM1 | ENST00000261606.11 | c.4615G>A | p.Gly1539Ser | missense_variant | 37/37 | 1 | A2 | ||
MYOM1 | ENST00000581804.1 | n.393G>A | non_coding_transcript_exon_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000591 AC: 90AN: 152236Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000467 AC: 117AN: 250512Hom.: 0 AF XY: 0.000458 AC XY: 62AN XY: 135458
GnomAD4 exome AF: 0.000902 AC: 1318AN: 1461244Hom.: 2 Cov.: 33 AF XY: 0.000867 AC XY: 630AN XY: 726906
GnomAD4 genome AF: 0.000591 AC: 90AN: 152354Hom.: 0 Cov.: 33 AF XY: 0.000564 AC XY: 42AN XY: 74502
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 11, 2022 | The p.G1635S variant (also known as c.4903G>A), located in coding exon 37 of the MYOM1 gene, results from a G to A substitution at nucleotide position 4903. The glycine at codon 1635 is replaced by serine, an amino acid with similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Hypertrophic cardiomyopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at