X-77830970-TTTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTA-TTTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTA

Variant names:

• chrX-77830970-T-TTTTTATTTTATTTTA
• rs201564456
• NM_001367916.1:c.902-90_902-76dupTAAAATAAAATAAAA

Variant summary

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

The NM_001367916.1(MAGT1):​c.902-90_902-76dupTAAAATAAAATAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000959 in 182,567 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 19 hemizygotes in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0018 (0 hom., 15 hem., cov: 0)
  • Exomes 𝑓: 0.00021 (0 hom. 4 hem.)
• Consequence: MAGT1 NM_001367916.1 intron
• Clinical Significance: Not reported in ClinVar
• 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 -4 ACMG points.

• BS2: High Hemizygotes in GnomAd4 at 15 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAGT1	NM_001367916.1	c.902-90_902-76dupTAAAATAAAATAAAA		intron_variant	Intron 8 of 9	ENST00000618282.5	NP_001354845.1
MAGT1	NM_032121.5	c.998-90_998-76dupTAAAATAAAATAAAA		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.902-76_902-75insTAAAATAAAATAAAA		intron_variant	Intron 8 of 9	1	NM_001367916.1	ENSP00000480732.1

Frequencies

GnomAD3 genomes AF: 0.00179 AC: 156 AN: 87205 Hom.: 0 Cov.: 0 AF XY: 0.000929 AC XY: 15 AN XY: 16139

Gnomad AFR AF: 0.00365

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000399

Gnomad ASJ AF: 0.00171

Gnomad EAS AF: 0.000683

Gnomad SAS AF: 0.00329

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00524

Gnomad NFE AF: 0.00120

Gnomad OTH AF: 0.000901

GnomAD4 exome AF: 0.000210 AC: 20 AN: 95365 Hom.: 0 AF XY: 0.000163 AC XY: 4 AN XY: 24525

Gnomad4 AFR exome AF: 0.000504

Gnomad4 AMR exome AF: 0.000269

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0000668

Gnomad4 NFE exome AF: 0.000266

Gnomad4 OTH exome AF: 0.000498

GnomAD4 genome AF: 0.00178 AC: 155 AN: 87202 Hom.: 0 Cov.: 0 AF XY: 0.000929 AC XY: 15 AN XY: 16148

Gnomad4 AFR AF: 0.00365

Gnomad4 AMR AF: 0.000398

Gnomad4 ASJ AF: 0.00171

Gnomad4 EAS AF: 0.000686

Gnomad4 SAS AF: 0.00332

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00120

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;