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NM_000051.4(ATM):c.2466+1G>A AND Hereditary cancer-predisposing syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Dec 26, 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:
RCV002431495.2

Allele description [Variation Report for NM_000051.4(ATM):c.2466+1G>A]

NM_000051.4(ATM):c.2466+1G>A

Gene:
ATM:ATM serine/threonine kinase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q22.3
Genomic location:
Preferred name:
NM_000051.4(ATM):c.2466+1G>A
HGVS:
  • NC_000011.10:g.108259076G>A
  • NG_009830.1:g.41245G>A
  • NM_000051.4:c.2466+1G>AMANE SELECT
  • NM_001351834.2:c.2466+1G>A
  • LRG_135t1:c.2466+1G>A
  • LRG_135:g.41245G>A
  • NC_000011.9:g.108129803G>A
  • NM_000051.3:c.2466+1G>A
Links:
dbSNP: rs914092098
NCBI 1000 Genomes Browser:
rs914092098
Molecular consequence:
  • NM_000051.4:c.2466+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001351834.2:c.2466+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002731670Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely pathogenic
(Dec 26, 2023) 		germlineclinical testing

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

Citation Link

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Summary from all submissions

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

Citations

PubMed

Splicing defects in the ataxia-telangiectasia gene, ATM: underlying mutations and consequences.

Teraoka SN, Telatar M, Becker-Catania S, Liang T, Onengüt S, Tolun A, Chessa L, Sanal O, Bernatowska E, Gatti RA, Concannon P.

Am J Hum Genet. 1999 Jun;64(6):1617-31.

PubMed [citation]
PMID:
10330348
PMCID:
PMC1377904

Details of each submission

From Ambry Genetics, SCV002731670.2

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

Description

The c.2466+1G>A intronic variant results from a G to A substitution one nucleotide after coding exon 15 of the ATM gene. This alteration was reported in a patient with a clinical diagnosis of ataxia-telangiectasia (A-T) with second mutation not identified (Teraoka SN et al. Am. J. Hum. Genet., 1999 Jun;64:1617-31). In addition, another alteration impacting the same donor site (c.2466+1delG) has been described in an individual with A-T in conjunctions with another pathogenic ATM mutation (Cavalieri S, Ann. Hum. Genet. 2008 Jan; 72(Pt 1):10-8). This variant is also known as IVS18+1G>A in the literature This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). Based on the majority of available evidence to date, this variant is likely to be pathogenic.

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

Last Updated: Sep 29, 2024