chrX-77830970-TTTTTA-T

Position:

• chrX-77830970-TTTTTA-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001367916.1(MAGT1):​c.902-80_902-76del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 181,983 control chromosomes in the GnomAD database, including 2,576 homozygotes. There are 3,732 hemizygotes in GnomAD. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.22 (2197 hom., 2475 hem., cov: 0)
  • Exomes 𝑓: 0.058 (379 hom. 1257 hem.)
• Consequence: MAGT1 NM_001367916.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.455

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 -10 ACMG points.

• BP6: Variant X-77830970-TTTTTA-T is Benign according to our data. Variant chrX-77830970-TTTTTA-T is described in ClinVar as [Benign]. Clinvar id is 1296390.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAGT1	NM_001367916.1	c.902-80_902-76del		intron_variant		ENST00000618282.5	NP_001354845.1
MAGT1	NM_032121.5	c.998-80_998-76del		intron_variant			NP_115497.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAGT1	ENST00000618282.5	c.902-80_902-76del		intron_variant		1	NM_001367916.1	ENSP00000480732	P1

Frequencies

GnomAD3 genomes AF: 0.218 AC: 18949 AN: 86927 Hom.: 2196 Cov.: 0 AF XY: 0.153 AC XY: 2468 AN XY: 16095

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.0521

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.00956

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.204

GnomAD4 exome AF: 0.0580 AC: 5516 AN: 95059 Hom.: 379 AF XY: 0.0515 AC XY: 1257 AN XY: 24405

Gnomad4 AFR exome AF: 0.0531

Gnomad4 AMR exome AF: 0.0277

Gnomad4 ASJ exome AF: 0.0190

Gnomad4 EAS exome AF: 0.00336

Gnomad4 SAS exome AF: 0.00567

Gnomad4 FIN exome AF: 0.156

Gnomad4 NFE exome AF: 0.0476

Gnomad4 OTH exome AF: 0.0472

GnomAD4 genome AF: 0.218 AC: 18959 AN: 86924 Hom.: 2197 Cov.: 0 AF XY: 0.154 AC XY: 2475 AN XY: 16104

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.00961

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.170

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.200

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

Nov 26, 2019

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs201564456; hg19: chrX-77086467;