X-77830970-TTTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTA-TTTTTA

Variant names:

• chrX-77830970-TTTTTATTTTATTTTATTTTATTTTATTTTATTTTA-T
• rs201564456
• NM_001367916.1:c.902-110_902-76delTAAAATAAAATAAAATAAAATAAAATAAAATAAAA

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001367916.1(MAGT1):​c.902-110_902-76delTAAAATAAAATAAAATAAAATAAAATAAAATAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00437 in 182,564 control chromosomes in the GnomAD database, including 20 homozygotes. There are 307 hemizygotes in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0023 (0 hom., 51 hem., cov: 0)
  • Exomes 𝑓: 0.0062 (20 hom. 256 hem.)
• Consequence: MAGT1 NM_001367916.1 intron
• Clinical Significance: Not reported in ClinVar
• 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 Likely_benign. Variant got -4 ACMG points.

• BS2: High Hemizygotes in GnomAd4 at 51 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAGT1	NM_001367916.1	c.902-110_902-76delTAAAATAAAATAAAATAAAATAAAATAAAATAAAA		intron_variant	Intron 8 of 9	ENST00000618282.5	NP_001354845.1
MAGT1	NM_032121.5	c.998-110_998-76delTAAAATAAAATAAAATAAAATAAAATAAAATAAAA		intron_variant	Intron 8 of 9		NP_115497.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAGT1	ENST00000618282.5	c.902-110_902-76delTAAAATAAAATAAAATAAAATAAAATAAAATAAAA		intron_variant	Intron 8 of 9	1	NM_001367916.1	ENSP00000480732.1

Frequencies

GnomAD3 genomes AF: 0.00233 AC: 203 AN: 87205 Hom.: 0 Cov.: 0 AF XY: 0.00316 AC XY: 51 AN XY: 16137

Gnomad AFR AF: 0.000343

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000399

Gnomad ASJ AF: 0.00128

Gnomad EAS AF: 0.000342

Gnomad SAS AF: 0.000548

Gnomad FIN AF: 0.0146

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00339

Gnomad OTH AF: 0.000901

GnomAD4 exome AF: 0.00623 AC: 594 AN: 95362 Hom.: 20 AF XY: 0.0104 AC XY: 256 AN XY: 24522

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00167

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000189

Gnomad4 FIN exome AF: 0.0149

Gnomad4 NFE exome AF: 0.00611

Gnomad4 OTH exome AF: 0.00448

GnomAD4 genome AF: 0.00233 AC: 203 AN: 87202 Hom.: 0 Cov.: 0 AF XY: 0.00316 AC XY: 51 AN XY: 16146

Gnomad4 AFR AF: 0.000343

Gnomad4 AMR AF: 0.000398

Gnomad4 ASJ AF: 0.00128

Gnomad4 EAS AF: 0.000343

Gnomad4 SAS AF: 0.000553

Gnomad4 FIN AF: 0.0146

Gnomad4 NFE AF: 0.00339

Gnomad4 OTH AF: 0.000887

ClinVar

Not reported in ClinVar

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;