chrX-77830970-T-TTTTTATTTTA

Position:

• chrX-77830970-T-TTTTTATTTTA

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_001367916.1(MAGT1):​c.902-76_902-75insTAAAATAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00131 in 95,360 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 31 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0094 (11 hom., 106 hem., cov: 0)
  • Exomes 𝑓: 0.0013 (0 hom. 31 hem.)
  • Failed GnomAD Quality Control
• Consequence: MAGT1 NM_001367916.1 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.701

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 Likely_benign. Variant got -6 ACMG points.

• BP6: Variant X-77830970-T-TTTTTATTTTA is Benign according to our data. Variant chrX-77830970-T-TTTTTATTTTA is described in ClinVar as [Likely_benign]. Clinvar id is 1211779.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Hemizygotes in GnomAdExome4 at 31 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAGT1	NM_001367916.1	c.902-76_902-75insTAAAATAAAA		intron_variant		ENST00000618282.5	NP_001354845.1
MAGT1	NM_032121.5	c.998-76_998-75insTAAAATAAAA		intron_variant			NP_115497.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAGT1	ENST00000618282.5	c.902-76_902-75insTAAAATAAAA		intron_variant		1	NM_001367916.1	ENSP00000480732	P1

Frequencies

GnomAD3 genomes AF: 0.00939 AC: 819 AN: 87185 Hom.: 11 Cov.: 0 AF XY: 0.00657 AC XY: 106 AN XY: 16137

Gnomad AFR AF: 0.0217

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00359

Gnomad ASJ AF: 0.00469

Gnomad EAS AF: 0.00376

Gnomad SAS AF: 0.0159

Gnomad FIN AF: 0.000885

Gnomad MID AF: 0.0157

Gnomad NFE AF: 0.00498

Gnomad OTH AF: 0.00541

GnomAD4 exome AF: 0.00131 AC: 125 AN: 95360 Hom.: 0 AF XY: 0.00126 AC XY: 31 AN XY: 24524

Gnomad4 AFR exome AF: 0.00353

Gnomad4 AMR exome AF: 0.00108

Gnomad4 ASJ exome AF: 0.00100

Gnomad4 EAS exome AF: 0.000560

Gnomad4 SAS exome AF: 0.00113

Gnomad4 FIN exome AF: 0.00160

Gnomad4 NFE exome AF: 0.00122

Gnomad4 OTH exome AF: 0.00224

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00939 AC: 819 AN: 87182 Hom.: 11 Cov.: 0 AF XY: 0.00657 AC XY: 106 AN XY: 16146

Gnomad4 AFR AF: 0.0216

Gnomad4 AMR AF: 0.00358

Gnomad4 ASJ AF: 0.00469

Gnomad4 EAS AF: 0.00378

Gnomad4 SAS AF: 0.0160

Gnomad4 FIN AF: 0.000885

Gnomad4 NFE AF: 0.00498

Gnomad4 OTH AF: 0.00621

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Oct 03, 2020

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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;