chr20-17969866-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_052865.4(MGME1):āc.7A>Gā(p.Met3Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000312 in 1,604,546 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. M3I) has been classified as Uncertain significance.
Frequency
Consequence
NM_052865.4 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 |
---|---|---|---|---|---|---|---|
MGME1 | NM_052865.4 | c.7A>G | p.Met3Val | missense_variant | 2/5 | ENST00000377710.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MGME1 | ENST00000377710.10 | c.7A>G | p.Met3Val | missense_variant | 2/5 | 1 | NM_052865.4 | P1 | |
MGME1 | ENST00000377709.1 | c.7A>G | p.Met3Val | missense_variant | 2/5 | 2 | |||
MGME1 | ENST00000377704.4 | c.7A>G | p.Met3Val | missense_variant | 2/3 | 3 | |||
OVOL2 | ENST00000486776.5 | n.492-12829T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152258Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000206 AC: 5AN: 242626Hom.: 0 AF XY: 0.0000304 AC XY: 4AN XY: 131658
GnomAD4 exome AF: 0.0000331 AC: 48AN: 1452288Hom.: 0 Cov.: 31 AF XY: 0.0000346 AC XY: 25AN XY: 722518
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152258Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74386
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 08, 2023 | The c.7A>G (p.M3V) alteration is located in exon 2 (coding exon 1) of the MGME1 gene. This alteration results from a A to G substitution at nucleotide position 7, causing the methionine (M) at amino acid position 3 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at