rs11551768
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_052865.4(MGME1):c.43A>T(p.Ser15Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 1,613,380 control chromosomes in the GnomAD database, including 11,807 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S15N) has been classified as Uncertain significance.
Frequency
Consequence
NM_052865.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MGME1 | NM_052865.4 | c.43A>T | p.Ser15Cys | missense_variant | 2/5 | ENST00000377710.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MGME1 | ENST00000377710.10 | c.43A>T | p.Ser15Cys | missense_variant | 2/5 | 1 | NM_052865.4 | P1 | |
MGME1 | ENST00000377709.1 | c.43A>T | p.Ser15Cys | missense_variant | 2/5 | 2 | |||
MGME1 | ENST00000377704.4 | c.43A>T | p.Ser15Cys | missense_variant | 2/3 | 3 | |||
OVOL2 | ENST00000486776.5 | n.492-12865T>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.100 AC: 15233AN: 152140Hom.: 861 Cov.: 33
GnomAD3 exomes AF: 0.102 AC: 25471AN: 250600Hom.: 1483 AF XY: 0.107 AC XY: 14564AN XY: 135606
GnomAD4 exome AF: 0.119 AC: 174276AN: 1461122Hom.: 10945 Cov.: 32 AF XY: 0.120 AC XY: 87320AN XY: 726930
GnomAD4 genome ? AF: 0.100 AC: 15230AN: 152258Hom.: 862 Cov.: 33 AF XY: 0.0973 AC XY: 7243AN XY: 74454
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Feb 22, 2016 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 16, 2015 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Mitochondrial DNA depletion syndrome 11 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at