rs876657892
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP2PP3_Moderate
The NM_002473.6(MYH9):āc.4598A>Gā(p.Gln1533Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,790 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q1533K) has been classified as Benign.
Frequency
Consequence
NM_002473.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYH9 | NM_002473.6 | c.4598A>G | p.Gln1533Arg | missense_variant | 33/41 | ENST00000216181.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYH9 | ENST00000216181.11 | c.4598A>G | p.Gln1533Arg | missense_variant | 33/41 | 1 | NM_002473.6 | P1 | |
MYH9 | ENST00000685801.1 | c.4661A>G | p.Gln1554Arg | missense_variant | 34/42 | ||||
MYH9 | ENST00000691109.1 | n.4893A>G | non_coding_transcript_exon_variant | 27/35 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461790Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 727202
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | The p.Gln1533Arg variant in MYH9 has not been reported previously in individuals with hearing loss, and was absent from large population studies. Computational prediction tools and conservation analyses do not provide strong evidence for or against an impact to the protein. In summary, the clinical significance of the p.Gln1533Arg variant is uncertain. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at