rs182757967
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_032121.5(MAGT1):c.67G>A(p.Val23Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00066 in 1,204,182 control chromosomes in the GnomAD database, including 2 homozygotes. There are 252 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_032121.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAGT1 | NM_032121.5 | c.67G>A | p.Val23Ile | missense_variant | 1/10 | NP_115497.4 | ||
MAGT1 | NM_001367916.1 | c.-30G>A | upstream_gene_variant | ENST00000618282.5 | NP_001354845.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAGT1 | ENST00000618282.5 | c.-30G>A | upstream_gene_variant | 1 | NM_001367916.1 | ENSP00000480732.1 |
Frequencies
GnomAD3 genomes AF: 0.000488 AC: 55AN: 112731Hom.: 1 Cov.: 24 AF XY: 0.000401 AC XY: 14AN XY: 34871
GnomAD3 exomes AF: 0.000677 AC: 114AN: 168288Hom.: 0 AF XY: 0.000599 AC XY: 33AN XY: 55108
GnomAD4 exome AF: 0.000678 AC: 740AN: 1091398Hom.: 1 Cov.: 31 AF XY: 0.000665 AC XY: 238AN XY: 357678
GnomAD4 genome AF: 0.000488 AC: 55AN: 112784Hom.: 1 Cov.: 24 AF XY: 0.000401 AC XY: 14AN XY: 34934
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Aug 16, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2022 | MAGT1: BP4 - |
MAGT1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 08, 2021 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at