rs2308327
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002412.5(MGMT):āc.533A>Gā(p.Lys178Arg) 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 1,613,358 control chromosomes in the GnomAD database, including 12,337 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002412.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MGMT | NM_002412.5 | c.533A>G | p.Lys178Arg | missense_variant | 5/5 | ENST00000651593.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MGMT | ENST00000651593.1 | c.533A>G | p.Lys178Arg | missense_variant | 5/5 | NM_002412.5 | P1 | ||
MGMT | ENST00000306010.8 | c.626A>G | p.Lys209Arg | missense_variant | 5/5 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0872 AC: 13274AN: 152220Hom.: 827 Cov.: 34
GnomAD3 exomes AF: 0.0937 AC: 23396AN: 249700Hom.: 1374 AF XY: 0.0979 AC XY: 13258AN XY: 135388
GnomAD4 exome AF: 0.120 AC: 174969AN: 1461020Hom.: 11511 Cov.: 32 AF XY: 0.119 AC XY: 86680AN XY: 726818
GnomAD4 genome ? AF: 0.0871 AC: 13270AN: 152338Hom.: 826 Cov.: 34 AF XY: 0.0857 AC XY: 6387AN XY: 74494
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 07, 2019 | This variant is associated with the following publications: (PMID: 17234722, 18812520) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at