chrX-77831066-G-A

Position:

• chrX-77831066-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001367916.1(MAGT1):​c.902-171C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.024 in 109,313 control chromosomes in the GnomAD database, including 77 homozygotes. There are 647 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.024 (77 hom., 647 hem., cov: 22)
• Consequence: MAGT1 NM_001367916.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.537

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP6: Variant X-77831066-G-A is Benign according to our data. Variant chrX-77831066-G-A is described in ClinVar as [Benign]. Clinvar id is 1253301.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0803 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAGT1	NM_001367916.1	c.902-171C>T		intron_variant		ENST00000618282.5	NP_001354845.1
MAGT1	NM_032121.5	c.998-171C>T		intron_variant			NP_115497.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAGT1	ENST00000618282.5	c.902-171C>T		intron_variant		1	NM_001367916.1	ENSP00000480732	P1

Frequencies

GnomAD3 genomes AF: 0.0240 AC: 2622 AN: 109266 Hom.: 77 Cov.: 22 AF XY: 0.0202 AC XY: 645 AN XY: 31968

Gnomad AFR AF: 0.0831

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00858

Gnomad ASJ AF: 0.00419

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000381

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00439

Gnomad NFE AF: 0.000228

Gnomad OTH AF: 0.0213

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0240 AC: 2624 AN: 109313 Hom.: 77 Cov.: 22 AF XY: 0.0202 AC XY: 647 AN XY: 32023

Gnomad4 AFR AF: 0.0830

Gnomad4 AMR AF: 0.00857

Gnomad4 ASJ AF: 0.00419

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000382

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000228

Gnomad4 OTH AF: 0.0211

Alfa AF: 0.0208 Hom.: 69

Bravo AF: 0.0280

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 08, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.88

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

Other links and lift over

dbSNP: rs187782730; hg19: chrX-77086563;