chr2-74462908-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000448666.7(MOGS):c.881C>T(p.Pro294Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000578 in 1,613,892 control chromosomes in the GnomAD database, including 7 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 Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P294A) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000448666.7 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MOGS | NM_006302.3 | c.881C>T | p.Pro294Leu | missense_variant | 4/4 | ENST00000448666.7 | NP_006293.2 | |
MOGS | NM_001146158.2 | c.563C>T | p.Pro188Leu | missense_variant | 5/5 | NP_001139630.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MOGS | ENST00000448666.7 | c.881C>T | p.Pro294Leu | missense_variant | 4/4 | 1 | NM_006302.3 | ENSP00000410992 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00290 AC: 442AN: 152224Hom.: 4 Cov.: 33
GnomAD3 exomes AF: 0.000675 AC: 168AN: 249036Hom.: 1 AF XY: 0.000488 AC XY: 66AN XY: 135220
GnomAD4 exome AF: 0.000336 AC: 491AN: 1461550Hom.: 3 Cov.: 31 AF XY: 0.000281 AC XY: 204AN XY: 727090
GnomAD4 genome AF: 0.00290 AC: 442AN: 152342Hom.: 4 Cov.: 33 AF XY: 0.00278 AC XY: 207AN XY: 74502
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Aug 29, 2017 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 09, 2016 | 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. - |
MOGS-congenital disorder of glycosylation Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 25, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at