X-77830970-TTTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTA-TTTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTA

Variant names:

• chrX-77830970-T-TTTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTA
• rs201564456
• NM_001367916.1:c.902-115_902-76dupTAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAA

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001367916.1(MAGT1):​c.902-115_902-76dupTAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00025 (0 hom., 0 hem., cov: 0)
  • Exomes 𝑓: 0.000031 (0 hom. 2 hem.)
  • Failed GnomAD Quality Control
• 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 Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAGT1	NM_001367916.1	c.902-115_902-76dupTAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAA		intron_variant	Intron 8 of 9	ENST00000618282.5	NP_001354845.1
MAGT1	NM_032121.5	c.998-115_998-76dupTAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAA		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_902-75insTAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAA		intron_variant	Intron 8 of 9	1	NM_001367916.1	ENSP00000480732.1

Frequencies

GnomAD3 genomes AF: 0.000252 AC: 22 AN: 87207 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 16139

Gnomad AFR AF: 0.0000429

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.000853

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000442

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000399

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000315 AC: 3 AN: 95366 Hom.: 0 AF XY: 0.0000815 AC XY: 2 AN XY: 24526

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000532

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.000252 AC: 22 AN: 87204 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 16148

Gnomad4 AFR AF: 0.0000429

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.000853

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000442

Gnomad4 NFE AF: 0.000399

Gnomad4 OTH AF: 0.00

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;