chr18-3215104-G-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_003803.4(MYOM1):āc.120C>Gā(p.Thr40=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000958 in 1,461,536 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 (ā ā ). Synonymous variant affecting the same amino acid position (i.e. T40T) has been classified as Likely benign.
Frequency
Consequence
NM_003803.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYOM1 | NM_003803.4 | c.120C>G | p.Thr40= | synonymous_variant | 2/38 | ENST00000356443.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYOM1 | ENST00000356443.9 | c.120C>G | p.Thr40= | synonymous_variant | 2/38 | 1 | NM_003803.4 | P2 | |
MYOM1 | ENST00000261606.11 | c.120C>G | p.Thr40= | synonymous_variant | 2/37 | 1 | A2 | ||
ENST00000580139.1 | n.198-1888G>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000806 AC: 2AN: 248166Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134920
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461536Hom.: 0 Cov.: 33 AF XY: 0.0000124 AC XY: 9AN XY: 727074
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Aug 13, 2015 | p.Thr40Thr in exon 2 of MYOM1: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue and is not located wit hin the splice consensus sequence. - |
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 19, 2020 | 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. - |
Hypertrophic cardiomyopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 25, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at