Genetic Variant MAGT1:c.902-95_902-76dupTAAAATAAAATAAAATAAAA (chrX-77830970-T-TTTTTATTTTATTTTATTTTA) – 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.902-95_902-76dupTAAAATAAAATAAAATAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_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 0.00071 ( 1 hom., 3 hem., cov: 0)

Exomes 𝑓: 0.00017 ( 0 hom. 5 hem. )

Failed GnomAD Quality Control

Consequence

MAGT1
NM_001367916.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.701

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BS2

High Hemizygotes in GnomAd4 at 3 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.902-95_902-76dupTAAAATAAAATAAAATAAAA		intron	N/A	NP_001354845.1	Q9H0U3-1
	MAGT1	NM_032121.5		c.998-95_998-76dupTAAAATAAAATAAAATAAAA		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.902-76_902-75insTAAAATAAAATAAAATAAAA	intron	N/A	ENSP00000480732.1	Q9H0U3-1
MAGT1	ENST00000358075.11	TSL:1	c.902-76_902-75insTAAAATAAAATAAAATAAAA	intron	N/A	ENSP00000354649.6	Q9H0U3-1
MAGT1	ENST00000685015.1		c.902-4162_902-4161insTAAAATAAAATAAAATAAAA	intron	N/A	ENSP00000509969.1	A0A8I5QKX7

Frequencies

GnomAD3 genomes

AF:

0.000711

AC:

AN:

87205

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000816

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000399

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00524

Gnomad NFE

AF:

0.000864

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000168

AC:

AN:

95366

Hom.:

AF XY:

0.000204

AC XY:

AN XY:

24526

show subpopulations

African (AFR)

AF:

0.000504

AC:

AN:

1984

American (AMR)

AF:

0.00

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:

0.000134

AC:

AN:

14965

Middle Eastern (MID)

AF:

0.00

AC:

AN:

605

European-Non Finnish (NFE)

AF:

0.000177

AC:

AN:

56427

Other (OTH)

AF:

0.000747

AC:

AN:

4015

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

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:

0.000711

AC:

AN:

87202

Hom.:

Cov.:

AF XY:

0.000186

AC XY:

AN XY:

16148

show subpopulations

African (AFR)

AF:

0.000815

AC:

AN:

23319

American (AMR)

AF:

0.000398

AC:

AN:

7535

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2346

East Asian (EAS)

AF:

0.00

AC:

AN:

2914

South Asian (SAS)

AF:

0.00

AC:

AN:

1809

European-Finnish (FIN)

AF:

0.00

AC:

AN:

2261

Middle Eastern (MID)

AF:

0.00581

AC:

AN:

172

European-Non Finnish (NFE)

AF:

0.000864

AC:

AN:

45142

Other (OTH)

AF:

0.00

AC:

AN:

1128

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.518

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

-0.70

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