rs182757967
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The ENST00000358075.11(MAGT1):c.-30G>A variant causes a 5 prime UTR 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. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00049 ( 1 hom., 14 hem., cov: 24)
Exomes 𝑓: 0.00068 ( 1 hom. 238 hem. )
Consequence
MAGT1
ENST00000358075.11 5_prime_UTR
ENST00000358075.11 5_prime_UTR
Scores
1
13
Clinical Significance
Conservation
PhyloP100: 2.04
Genes affected
MAGT1 (HGNC:28880): (magnesium transporter 1) This gene encodes a ubiquitously expressed magnesium cation transporter protein that localizes to the cell membrane. This protein also associates with N-oligosaccharyl transferase and therefore may have a role in N-glycosylation. Mutations in this gene cause a form of X-linked intellectual disability (XLID). This gene may have multiple in-frame translation initiation sites, one of which would encode a shorter protein with an N-terminus containing a signal peptide at amino acids 1-29. [provided by RefSeq, Jul 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.016403139).
BP6
?
Variant X-77895440-C-T is Benign according to our data. Variant chrX-77895440-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 445825.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-77895440-C-T is described in Lovd as [Likely_benign].
BS2
?
High Hemizygotes in GnomAd4 at 14 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAGT1 | NM_032121.5 | c.67G>A | p.Val23Ile | missense_variant | 1/10 | ||
MAGT1 | NM_001367916.1 | upstream_gene_variant | ENST00000618282.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAGT1 | ENST00000618282.5 | upstream_gene_variant | 1 | NM_001367916.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000488 AC: 55AN: 112731Hom.: 1 Cov.: 24 AF XY: 0.000401 AC XY: 14AN XY: 34871
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GnomAD3 exomes AF: 0.000677 AC: 114AN: 168288Hom.: 0 AF XY: 0.000599 AC XY: 33AN XY: 55108
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GnomAD4 exome AF: 0.000678 AC: 740AN: 1091398Hom.: 1 Cov.: 31 AF XY: 0.000665 AC XY: 238AN XY: 357678
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GnomAD4 genome ? AF: 0.000488 AC: 55AN: 112784Hom.: 1 Cov.: 24 AF XY: 0.000401 AC XY: 14AN XY: 34934
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
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, criteria provided, single submitter | 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 | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T
FATHMM_MKL
Benign
N
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;N
PrimateAI
Benign
T
PROVEAN
Benign
N;.
REVEL
Benign
Sift
Benign
T;.
Sift4G
Benign
T;T
Vest4
MVP
MPC
ClinPred
T
GERP RS
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at