NM_000051.4(ATM):c.5917A>C (p.Arg1973=) AND Ataxia-telangiectasia syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 12, 2023
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:: RCV002559091.10

Allele description [Variation Report for NM_000051.4(ATM):c.5917A>C (p.Arg1973=)]

NM_000051.4(ATM):c.5917A>C (p.Arg1973=)

Genes:

ATM:ATM serine/threonine kinase [Gene - OMIM - HGNC]
C11orf65:chromosome 11 open reading frame 65 [Gene - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q22.3

Genomic location:

Preferred name:

NM_000051.4(ATM):c.5917A>C (p.Arg1973=)

HGVS:

NC_000011.10:g.108310314A>C
NG_009830.1:g.92483A>C
NG_054724.1:g.164519T>G
NM_000051.4:c.5917A>CMANE SELECT
NM_001330368.2:c.641-1243T>G
NM_001351110.2:c.*39-1243T>G
NM_001351834.2:c.5917A>C
NP_000042.3:p.Arg1973=
NP_000042.3:p.Arg1973=
NP_001338763.1:p.Arg1973=
LRG_135t1:c.5917A>C
LRG_135:g.92483A>C
LRG_135p1:p.Arg1973=
NC_000011.9:g.108181041A>C
NC_000011.9:g.108181041A>C
NM_000051.3:c.5917A>C

Links:

dbSNP: rs786202089

NCBI 1000 Genomes Browser:

rs786202089

Molecular consequence:

NM_001330368.2:c.641-1243T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001351110.2:c.*39-1243T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_000051.4:c.5917A>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001351834.2:c.5917A>C - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: Ataxia-telangiectasia syndrome (AT)
Synonyms:: Louis-Bar syndrome; Cerebello-oculocutaneous telangiectasia; Immunodeficiency with ataxia telangiectasia; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0008840; MedGen: C0004135; Orphanet: 100; OMIM: 208900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003467498	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 12, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003467498

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 12, 2023)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Nothing to display

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003467498.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This sequence change affects codon 1973 of the ATM mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the ATM protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (no rsID available, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with ATM-related conditions. ClinVar contains an entry for this variant (Variation ID: 924458). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 18, 2024

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