Genetic Variant MAGT1:c.902-90_902-76dupTAAAATAAAATAAAA (chrX-77830970-T-TTTTTATTTTATTTTA) – 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.902-90_902-76dupTAAAATAAAATAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000959 in 182,567 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 19 hemizygotes in GnomAD. 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 0.0018 ( 0 hom., 15 hem., cov: 0)

Exomes 𝑓: 0.00021 ( 0 hom. 4 hem. )

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 15 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.902-90_902-76dupTAAAATAAAATAAAA		intron	N/A	NP_001354845.1	Q9H0U3-1
	MAGT1	NM_032121.5		c.998-90_998-76dupTAAAATAAAATAAAA		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_902-75insTAAAATAAAATAAAA	intron	N/A	ENSP00000480732.1	Q9H0U3-1
MAGT1	ENST00000358075.11	TSL:1	c.902-76_902-75insTAAAATAAAATAAAA	intron	N/A	ENSP00000354649.6	Q9H0U3-1
MAGT1	ENST00000685015.1		c.902-4162_902-4161insTAAAATAAAATAAAA	intron	N/A	ENSP00000509969.1	A0A8I5QKX7

Frequencies

GnomAD3 genomes

AF:

0.00179

AC:

156

AN:

87205

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00365

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000399

Gnomad ASJ

AF:

0.00171

Gnomad EAS

AF:

0.000683

Gnomad SAS

AF:

0.00329

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00524

Gnomad NFE

AF:

0.00120

Gnomad OTH

AF:

0.000901

GnomAD4 exome

AF:

0.000210

AC:

AN:

95365

Hom.:

AF XY:

0.000163

AC XY:

AN XY:

24525

show subpopulations

African (AFR)

AF:

0.000504

AC:

AN:

1984

American (AMR)

AF:

0.000269

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:

0.0000668

AC:

AN:

14965

Middle Eastern (MID)

AF:

0.00

AC:

AN:

605

European-Non Finnish (NFE)

AF:

0.000266

AC:

AN:

56426

Other (OTH)

AF:

0.000498

AC:

AN:

4015

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.438

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.00178

AC:

155

AN:

87202

Hom.:

Cov.:

AF XY:

0.000929

AC XY:

AN XY:

16148

show subpopulations

African (AFR)

AF:

0.00365

AC:

AN:

23319

American (AMR)

AF:

0.000398

AC:

AN:

7535

Ashkenazi Jewish (ASJ)

AF:

0.00171

AC:

AN:

2346

East Asian (EAS)

AF:

0.000686

AC:

AN:

2914

South Asian (SAS)

AF:

0.00332

AC:

AN:

1809

European-Finnish (FIN)

AF:

0.00

AC:

AN:

2261

Middle Eastern (MID)

AF:

0.00

AC:

AN:

172

European-Non Finnish (NFE)

AF:

0.00120

AC:

AN:

45142

Other (OTH)

AF:

0.000887

AC:

AN:

1128

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.513

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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X-77830970-TTTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTA-TTTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTA

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