rs199900004
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_003803.4(MYOM1):āc.2656A>Gā(p.Ser886Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00097 in 1,614,010 control chromosomes in the GnomAD database, including 1 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 Likely benign (ā ā ).
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYOM1 | NM_003803.4 | c.2656A>G | p.Ser886Gly | missense_variant | 18/38 | ENST00000356443.9 | NP_003794.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYOM1 | ENST00000356443.9 | c.2656A>G | p.Ser886Gly | missense_variant | 18/38 | 1 | NM_003803.4 | ENSP00000348821.4 | ||
MYOM1 | ENST00000261606.11 | c.2506+2005A>G | intron_variant | 1 | ENSP00000261606.7 | |||||
MYOM1 | ENST00000582016.1 | n.212A>G | non_coding_transcript_exon_variant | 1/3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.000506 AC: 77AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000590 AC: 147AN: 249258Hom.: 0 AF XY: 0.000614 AC XY: 83AN XY: 135220
GnomAD4 exome AF: 0.00102 AC: 1489AN: 1461704Hom.: 1 Cov.: 31 AF XY: 0.000974 AC XY: 708AN XY: 727134
GnomAD4 genome AF: 0.000506 AC: 77AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.000510 AC XY: 38AN XY: 74480
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | May 26, 2015 | p.Ser886Gly in exon 18 of MYOM1: This variant is not expected to have clinical s ignificance due to a lack of conservation across species, including mammals. Of note, 4 mammals (alpaca, Bactrian camel, cape golden mole and platypus) have a g lycine (Gly) at this position despite high nearby amino acid conservation. It h as been identified in 0.1% (59/66740) of European chromosomes by the Exome Aggre gation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs199900004). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Hypertrophic cardiomyopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 22, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at