X-77830970-TTTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTA-TTTTTATTTTATTTTA

Variant names:

• chrX-77830970-TTTTTATTTTATTTTATTTTATTTTA-T
• rs201564456
• NM_001367916.1:c.902-100_902-76delTAAAATAAAATAAAATAAAATAAAA

Variant summary

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

The NM_001367916.1(MAGT1):​c.902-100_902-76delTAAAATAAAATAAAATAAAATAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00224 in 182,260 control chromosomes in the GnomAD database, including 2 homozygotes. There are 85 hemizygotes in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0032 (2 hom., 45 hem., cov: 0)
  • Exomes 𝑓: 0.0014 (0 hom. 40 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 Homozygotes in GnomAd4 at 2 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAGT1	NM_001367916.1	c.902-100_902-76delTAAAATAAAATAAAATAAAATAAAA		intron_variant	Intron 8 of 9	ENST00000618282.5	NP_001354845.1
MAGT1	NM_032121.5	c.998-100_998-76delTAAAATAAAATAAAATAAAATAAAA		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.902-100_902-76delTAAAATAAAATAAAATAAAATAAAA		intron_variant	Intron 8 of 9	1	NM_001367916.1	ENSP00000480732.1

Frequencies

GnomAD3 genomes AF: 0.00318 AC: 277 AN: 87198 Hom.: 2 Cov.: 0 AF XY: 0.00279 AC XY: 45 AN XY: 16136

Gnomad AFR AF: 0.00863

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00252

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000442

Gnomad MID AF: 0.00524

Gnomad NFE AF: 0.00113

Gnomad OTH AF: 0.00360

GnomAD4 exome AF: 0.00137 AC: 130 AN: 95065 Hom.: 0 AF XY: 0.00164 AC XY: 40 AN XY: 24383

Gnomad4 AFR exome AF: 0.00706

Gnomad4 AMR exome AF: 0.00216

Gnomad4 ASJ exome AF: 0.000669

Gnomad4 EAS exome AF: 0.000748

Gnomad4 SAS exome AF: 0.000189

Gnomad4 FIN exome AF: 0.000268

Gnomad4 NFE exome AF: 0.00164

Gnomad4 OTH exome AF: 0.00125

GnomAD4 genome AF: 0.00319 AC: 278 AN: 87195 Hom.: 2 Cov.: 0 AF XY: 0.00279 AC XY: 45 AN XY: 16145

Gnomad4 AFR AF: 0.00866

Gnomad4 AMR AF: 0.00252

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000442

Gnomad4 NFE AF: 0.00113

Gnomad4 OTH AF: 0.00355

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;