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NC_000023.10:g.(?_76972588)_(77084752_?)dup AND X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 14, 2022
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003122854.5

Allele description [Variation Report for NC_000023.10:g.(?_76972588)_(77084752_?)dup]

NC_000023.10:g.(?_76972588)_(77084752_?)dup

Genes:
ATRX:ATRX chromatin remodeler [Gene - OMIM - HGNC]
MAGT1:magnesium transporter 1 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
Xq21.1
Genomic location:
ChrX: 76972588 - 77084752 (on Assembly GRCh37)
Preferred name:
NC_000023.10:g.(?_76972588)_(77084752_?)dup
HGVS:
NC_000023.10:g.(?_76972588)_(77084752_?)dup

Condition(s)

Name:
X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection and neoplasia
Identifiers:
MONDO: MONDO:0010455; MedGen: C3275445; Orphanet: 317476; OMIM: 300853

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003795712Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Sep 14, 2022) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003795712.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant has not been reported in the literature in individuals affected with MAGT1-related conditions. This variant results in a copy number gain of the genomic region encompassing exon(s) 10 of the MAGT1 gene. This region includes the termination codon of the gene. This copy number gain extends beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024