chr3-155084192-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_007289.4(MME):āc.25G>Cā(p.Asp9His) variant causes a missense change. The variant allele was found at a frequency of 0.00000372 in 1,613,884 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. D9G) has been classified as Uncertain significance.
Frequency
Consequence
NM_007289.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MME | NM_007289.4 | c.25G>C | p.Asp9His | missense_variant | 2/23 | ENST00000360490.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MME | ENST00000360490.7 | c.25G>C | p.Asp9His | missense_variant | 2/23 | 1 | NM_007289.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152044Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251436Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135902
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461840Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727224
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152044Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74276
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 29, 2021 | This sequence change replaces aspartic acid, which is acidic and polar, with histidine, which is basic and polar, at codon 9 of the MME protein (p.Asp9His). This variant is present in population databases (rs370911005, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with MME-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at