Variant X-77830760-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_001367916.1(MAGT1):c.992+45G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0151 in 711,725 control chromosomes in the GnomAD database, including 86 homozygotes. There are 2,788 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.011 ( 9 hom., 360 hem., cov: 23)

Exomes 𝑓: 0.016 ( 77 hom. 2428 hem. )

Consequence

MAGT1
NM_001367916.1 intron

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.29

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant X-77830760-C-T is Benign according to our data. Variant chrX-77830760-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1216721.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0114 (1252/110200) while in subpopulation NFE AF= 0.0184 (967/52676). AF 95% confidence interval is 0.0174. There are 9 homozygotes in gnomad4. There are 360 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 9 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAGT1	NM_001367916.1 linkuse as main transcript	c.992+45G>A		intron_variant		ENST00000618282.5	NP_001354845.1
MAGT1	NM_032121.5 linkuse as main transcript	c.1088+45G>A		intron_variant			NP_115497.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAGT1	ENST00000618282.5 linkuse as main transcript	c.992+45G>A		intron_variant		1	NM_001367916.1	ENSP00000480732	P1	Q9H0U3-1

Frequencies

GnomAD3 genomes

AF:

0.0114

AC:

1252

AN:

110166

Hom.:

Cov.:

AF XY:

0.0110

AC XY:

360

AN XY:

32830

show subpopulations

Gnomad AFR

AF:

0.00222

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00906

Gnomad ASJ

AF:

0.00381

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0163

Gnomad FIN

AF:

0.00967

Gnomad MID

AF:

0.00431

Gnomad NFE

AF:

0.0184

Gnomad OTH

AF:

0.0121

GnomAD3 exomes

AF:

0.0115

AC:

1668

AN:

144901

Hom.:

AF XY:

0.0119

AC XY:

507

AN XY:

42583

show subpopulations

Gnomad AFR exome

AF:

0.00189

Gnomad AMR exome

AF:

0.00357

Gnomad ASJ exome

AF:

0.00371

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0157

Gnomad FIN exome

AF:

0.00947

Gnomad NFE exome

AF:

0.0176

Gnomad OTH exome

AF:

0.0106

GnomAD4 exome

AF:

0.0158

AC:

9513

AN:

601525

Hom.:

Cov.:

AF XY:

0.0154

AC XY:

2428

AN XY:

157199

show subpopulations

Gnomad4 AFR exome

AF:

0.00126

Gnomad4 AMR exome

AF:

0.00399

Gnomad4 ASJ exome

AF:

0.00316

Gnomad4 EAS exome

AF:

0.0000835

Gnomad4 SAS exome

AF:

0.0171

Gnomad4 FIN exome

AF:

0.0107

Gnomad4 NFE exome

AF:

0.0191

Gnomad4 OTH exome

AF:

0.0115

GnomAD4 genome

AF:

0.0114

AC:

1252

AN:

110200

Hom.:

Cov.:

AF XY:

0.0110

AC XY:

360

AN XY:

32874

show subpopulations

Gnomad4 AFR

AF:

0.00221

Gnomad4 AMR

AF:

0.00905

Gnomad4 ASJ

AF:

0.00381

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0164

Gnomad4 FIN

AF:

0.00967

Gnomad4 NFE

AF:

0.0184

Gnomad4 OTH

AF:

0.0119

Alfa

AF:

0.0153

Hom.:

168

Bravo

AF:

0.0110

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 31, 2020	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.11

DANN

Benign

0.38

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over