chrX-77830970-TTTTTATTTTA-T

Position:

• chrX-77830970-TTTTTATTTTA-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001367916.1(MAGT1):​c.902-85_902-76del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0209 in 182,396 control chromosomes in the GnomAD database, including 115 homozygotes. There are 644 hemizygotes in GnomAD. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.033 (89 hom., 398 hem., cov: 0)
  • Exomes 𝑓: 0.0097 (26 hom. 246 hem.)
• Consequence: MAGT1 NM_001367916.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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 Benign. Variant got -10 ACMG points.

• BP6: Variant X-77830970-TTTTTATTTTA-T is Benign according to our data. Variant chrX-77830970-TTTTTATTTTA-T is described in ClinVar as [Benign]. Clinvar id is 1241523.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAGT1	NM_001367916.1	c.902-85_902-76del		intron_variant		ENST00000618282.5	NP_001354845.1
MAGT1	NM_032121.5	c.998-85_998-76del		intron_variant			NP_115497.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAGT1	ENST00000618282.5	c.902-85_902-76del		intron_variant		1	NM_001367916.1	ENSP00000480732	P1

Frequencies

GnomAD3 genomes AF: 0.0330 AC: 2877 AN: 87158 Hom.: 89 Cov.: 0 AF XY: 0.0246 AC XY: 396 AN XY: 16126

Gnomad AFR AF: 0.0668

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0443

Gnomad ASJ AF: 0.0277

Gnomad EAS AF: 0.0955

Gnomad SAS AF: 0.0340

Gnomad FIN AF: 0.0257

Gnomad MID AF: 0.0209

Gnomad NFE AF: 0.0108

Gnomad OTH AF: 0.0324

GnomAD4 exome AF: 0.00973 AC: 927 AN: 95241 Hom.: 26 AF XY: 0.0101 AC XY: 246 AN XY: 24443

Gnomad4 AFR exome AF: 0.0167

Gnomad4 AMR exome AF: 0.00592

Gnomad4 ASJ exome AF: 0.00534

Gnomad4 EAS exome AF: 0.0523

Gnomad4 SAS exome AF: 0.00189

Gnomad4 FIN exome AF: 0.0210

Gnomad4 NFE exome AF: 0.00362

Gnomad4 OTH exome AF: 0.0115

GnomAD4 genome AF: 0.0330 AC: 2880 AN: 87155 Hom.: 89 Cov.: 0 AF XY: 0.0247 AC XY: 398 AN XY: 16135

Gnomad4 AFR AF: 0.0668

Gnomad4 AMR AF: 0.0442

Gnomad4 ASJ AF: 0.0277

Gnomad4 EAS AF: 0.0956

Gnomad4 SAS AF: 0.0343

Gnomad4 FIN AF: 0.0257

Gnomad4 NFE AF: 0.0108

Gnomad4 OTH AF: 0.0328

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 07, 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;