Genetic Variant MAGT1:c.902-115_902-76delTAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAA (chrX-77830970-TTTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTA-T) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_001367916.1(MAGT1):c.902-115_902-76delTAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000438 in 182,571 control chromosomes in the GnomAD database, including 2 homozygotes. There are 2 hemizygotes in GnomAD. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000011 ( 0 hom., 1 hem., cov: 0)

Exomes 𝑓: 0.000073 ( 2 hom. 1 hem. )

Consequence

MAGT1
NM_001367916.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.455

Publications

0 publications found

Variant links:

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]

MAGT1 Gene-Disease associations (from GenCC):

X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia
Inheritance: XL, Unknown Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet
intellectual disability, X-linked 95
Inheritance: XL Classification: LIMITED Submitted by: G2P
X-linked intellectual disability
Inheritance: XL Classification: NO_KNOWN Submitted by: ClinGen

MAGT1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2

High Homozygotes in GnomAdExome4 at 2 XL,Unknown gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001367916.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAGT1	NM_001367916.1	MANE Select	c.902-115_902-76delTAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAA		intron	N/A	NP_001354845.1	Q9H0U3-1
	MAGT1	NM_032121.5		c.998-115_998-76delTAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAA		intron	N/A	NP_115497.4	Q9H0U3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MAGT1	ENST00000618282.5	TSL:1 MANE Select	c.902-115_902-76delTAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAA	intron	N/A	ENSP00000480732.1	Q9H0U3-1
MAGT1	ENST00000358075.11	TSL:1	c.902-115_902-76delTAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAA	intron	N/A	ENSP00000354649.6	Q9H0U3-1
MAGT1	ENST00000685015.1		c.902-4201_902-4162delTAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAA	intron	N/A	ENSP00000509969.1	A0A8I5QKX7

Frequencies

GnomAD3 genomes

AF:

0.0000115

AC:

AN:

87207

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000221

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0000734

AC:

AN:

95364

Hom.:

AF XY:

0.0000408

AC XY:

AN XY:

24524

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

1984

American (AMR)

AF:

0.000807

AC:

AN:

3719

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2998

East Asian (EAS)

AF:

0.00

AC:

AN:

5359

South Asian (SAS)

AF:

0.00

AC:

AN:

5294

European-Finnish (FIN)

AF:

0.00

AC:

AN:

14965

Middle Eastern (MID)

AF:

0.00

AC:

AN:

605

European-Non Finnish (NFE)

AF:

0.0000709

AC:

AN:

56425

Other (OTH)

AF:

0.00

AC:

AN:

4015

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.800

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0000115

AC:

AN:

87207

Hom.:

Cov.:

AF XY:

0.0000620

AC XY:

AN XY:

16139

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

23296

American (AMR)

AF:

0.00

AC:

AN:

7526

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2346

East Asian (EAS)

AF:

0.00

AC:

AN:

2928

South Asian (SAS)

AF:

0.00

AC:

AN:

1825

European-Finnish (FIN)

AF:

0.00

AC:

AN:

2261

Middle Eastern (MID)

AF:

0.00

AC:

AN:

191

European-Non Finnish (NFE)

AF:

0.0000221

AC:

AN:

45148

Other (OTH)

AF:

0.00

AC:

AN:

1110

Alfa

AF:

0.00

Hom.:

943

Bravo

AF:

0.0000151

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.46

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over