Genetic Variant MAGT1:c.902-100_902-76delTAAAATAAAATAAAATAAAATAAAA (chrX-77830970-TTTTTATTTTATTTTATTTTATTTTA-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.902-100_902-76delTAAAATAAAATAAAATAAAATAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00224 in 182,260 control chromosomes in the GnomAD database, including 2 homozygotes. There are 85 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 0.0032 ( 2 hom., 45 hem., cov: 0)

Exomes 𝑓: 0.0014 ( 0 hom. 40 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 GnomAd4 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.902-100_902-76delTAAAATAAAATAAAATAAAATAAAA		intron	N/A	NP_001354845.1	Q9H0U3-1
	MAGT1	NM_032121.5		c.998-100_998-76delTAAAATAAAATAAAATAAAATAAAA		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.902-100_902-76delTAAAATAAAATAAAATAAAATAAAA	intron	N/A	ENSP00000480732.1	Q9H0U3-1
MAGT1	ENST00000358075.11	TSL:1	c.902-100_902-76delTAAAATAAAATAAAATAAAATAAAA	intron	N/A	ENSP00000354649.6	Q9H0U3-1
MAGT1	ENST00000685015.1		c.902-4186_902-4162delTAAAATAAAATAAAATAAAATAAAA	intron	N/A	ENSP00000509969.1	A0A8I5QKX7

Frequencies

GnomAD3 genomes

AF:

0.00318

AC:

277

AN:

87198

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00863

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00252

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000442

Gnomad MID

AF:

0.00524

Gnomad NFE

AF:

0.00113

Gnomad OTH

AF:

0.00360

GnomAD4 exome

AF:

0.00137

AC:

130

AN:

95065

Hom.:

AF XY:

0.00164

AC XY:

AN XY:

24383

show subpopulations

African (AFR)

AF:

0.00706

AC:

AN:

1984

American (AMR)

AF:

0.00216

AC:

AN:

3706

Ashkenazi Jewish (ASJ)

AF:

0.000669

AC:

AN:

2990

East Asian (EAS)

AF:

0.000748

AC:

AN:

5349

South Asian (SAS)

AF:

0.000189

AC:

AN:

5290

European-Finnish (FIN)

AF:

0.000268

AC:

AN:

14931

Middle Eastern (MID)

AF:

0.00

AC:

AN:

604

European-Non Finnish (NFE)

AF:

0.00164

AC:

AN:

56206

Other (OTH)

AF:

0.00125

AC:

AN:

4005

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.428

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00319

AC:

278

AN:

87195

Hom.:

Cov.:

AF XY:

0.00279

AC XY:

AN XY:

16145

show subpopulations

African (AFR)

AF:

0.00866

AC:

202

AN:

23319

American (AMR)

AF:

0.00252

AC:

AN:

7535

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2346

East Asian (EAS)

AF:

0.00

AC:

AN:

2912

South Asian (SAS)

AF:

0.00

AC:

AN:

1809

European-Finnish (FIN)

AF:

0.000442

AC:

AN:

2261

Middle Eastern (MID)

AF:

0.00581

AC:

AN:

172

European-Non Finnish (NFE)

AF:

0.00113

AC:

AN:

45137

Other (OTH)

AF:

0.00355

AC:

AN:

1128

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.531

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

943

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.46

Mutation Taster

=100/0

polymorphism

(source)

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

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over