rs61732679
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001367916.1(MAGT1):c.651T>A(p.Thr217=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00285 in 1,207,966 control chromosomes in the GnomAD database, including 51 homozygotes. There are 889 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.015 ( 27 hom., 430 hem., cov: 23)
Exomes 𝑓: 0.0016 ( 24 hom. 459 hem. )
Consequence
MAGT1
NM_001367916.1 synonymous
NM_001367916.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.35
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 -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP6
?
Variant X-77856754-A-T is Benign according to our data. Variant chrX-77856754-A-T is described in ClinVar as [Benign]. Clinvar id is 129568.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=3.35 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.015 (1678/111891) while in subpopulation AFR AF= 0.0514 (1587/30856). AF 95% confidence interval is 0.0493. There are 27 homozygotes in gnomad4. There are 430 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 27 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAGT1 | NM_001367916.1 | c.651T>A | p.Thr217= | synonymous_variant | 5/10 | ENST00000618282.5 | |
MAGT1 | NM_032121.5 | c.747T>A | p.Thr249= | synonymous_variant | 5/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAGT1 | ENST00000618282.5 | c.651T>A | p.Thr217= | synonymous_variant | 5/10 | 1 | NM_001367916.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0150 AC: 1676AN: 111837Hom.: 27 Cov.: 23 AF XY: 0.0126 AC XY: 429AN XY: 34027
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GnomAD3 exomes AF: 0.00449 AC: 820AN: 182455Hom.: 12 AF XY: 0.00268 AC XY: 180AN XY: 67165
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GnomAD4 exome AF: 0.00161 AC: 1770AN: 1096075Hom.: 24 Cov.: 28 AF XY: 0.00127 AC XY: 459AN XY: 361585
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GnomAD4 genome ? AF: 0.0150 AC: 1678AN: 111891Hom.: 27 Cov.: 23 AF XY: 0.0126 AC XY: 430AN XY: 34091
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 06, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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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