X-77830970-TTTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTA-TTTTTATTTTATTTTATTTTATTTTATTTTA

Variant names:

• chrX-77830970-TTTTTATTTTA-T
• rs201564456
• NM_001367916.1:c.902-85_902-76delTAAAATAAAA

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001367916.1(MAGT1):​c.902-85_902-76delTAAAATAAAA 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
• Publications: 0 publications found

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]

MAGT1 Gene-Disease associations (from GenCC):

• X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia

  Inheritance: XL, Unknown Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet
• intellectual disability, X-linked 95

  Inheritance: XL Classification: LIMITED Submitted by: G2P
• X-linked intellectual disability

  Inheritance: XL Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001367916.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAGT1	NM_001367916.1	MANE Select	c.902-85_902-76delTAAAATAAAA		intron	N/A	NP_001354845.1	Q9H0U3-1
	MAGT1	NM_032121.5		c.998-85_998-76delTAAAATAAAA		intron	N/A	NP_115497.4	Q9H0U3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAGT1	ENST00000618282.5	TSL:1 MANE Select	c.902-85_902-76delTAAAATAAAA		intron	N/A	ENSP00000480732.1	Q9H0U3-1
	MAGT1	ENST00000358075.11	TSL:1	c.902-85_902-76delTAAAATAAAA		intron	N/A	ENSP00000354649.6	Q9H0U3-1
	MAGT1	ENST00000685015.1		c.902-4171_902-4162delTAAAATAAAA		intron	N/A	ENSP00000509969.1	A0A8I5QKX7

Frequencies

GnomAD3 genomes AF: 0.0330 AC: 2877 AN: 87158 Hom.: 89 Cov.: 0

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

African (AFR) AF: 0.0167 AC: 33 AN: 1981

American (AMR) AF: 0.00592 AC: 22 AN: 3715

Ashkenazi Jewish (ASJ) AF: 0.00534 AC: 16 AN: 2996

East Asian (EAS) AF: 0.0523 AC: 280 AN: 5350

South Asian (SAS) AF: 0.00189 AC: 10 AN: 5294

European-Finnish (FIN) AF: 0.0210 AC: 313 AN: 14910

Middle Eastern (MID) AF: 0.00496 AC: 3 AN: 605

European-Non Finnish (NFE) AF: 0.00362 AC: 204 AN: 56379

Other (OTH) AF: 0.0115 AC: 46 AN: 4011

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

African (AFR) AF: 0.0668 AC: 1557 AN: 23293

American (AMR) AF: 0.0442 AC: 333 AN: 7526

Ashkenazi Jewish (ASJ) AF: 0.0277 AC: 65 AN: 2346

East Asian (EAS) AF: 0.0956 AC: 278 AN: 2908

South Asian (SAS) AF: 0.0343 AC: 62 AN: 1809

European-Finnish (FIN) AF: 0.0257 AC: 58 AN: 2259

Middle Eastern (MID) AF: 0.0233 AC: 4 AN: 172

European-Non Finnish (NFE) AF: 0.0108 AC: 486 AN: 45138

Other (OTH) AF: 0.0328 AC: 37 AN: 1128

Alfa AF: 0.0187 Hom.: 943

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.46
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs201564456; hg19: chrX-77086467;