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NM_000051.4(ATM):c.2467G>T (p.Ala823Ser) AND Hereditary cancer-predisposing syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 30, 2014
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:
RCV000165954.3

Allele description [Variation Report for NM_000051.4(ATM):c.2467G>T (p.Ala823Ser)]

NM_000051.4(ATM):c.2467G>T (p.Ala823Ser)

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.2467G>T (p.Ala823Ser)
HGVS:
  • NC_000011.10:g.108267171G>T
  • NG_009830.1:g.49340G>T
  • NM_000051.4:c.2467G>TMANE SELECT
  • NM_001351834.2:c.2467G>T
  • NP_000042.3:p.Ala823Ser
  • NP_000042.3:p.Ala823Ser
  • NP_001338763.1:p.Ala823Ser
  • LRG_135t1:c.2467G>T
  • LRG_135:g.49340G>T
  • LRG_135p1:p.Ala823Ser
  • NC_000011.9:g.108137898G>T
  • NM_000051.3:c.2467G>T
  • p.A823S
Protein change:
A823S
Links:
dbSNP: rs786202895
NCBI 1000 Genomes Browser:
rs786202895
Molecular consequence:
  • NM_000051.4:c.2467G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001351834.2:c.2467G>T - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000216711Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Uncertain significance
(Sep 30, 2014) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Ambry Genetics, SCV000216711.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The p.A823S variant (also known as c.2467G>T) is located in coding exon 16 of the ATM gene. The alanine at codon 823 is replaced by serine, an amino acid with similar properties. This change occurs in the first base pair of coding exon 16 which makes it likely to have some effect on normal mRNA splicing. Using two different splice site prediction tools, this alteration is predicted by ESEfinder to weaken the efficacy of the native acceptor splice site, but is not predicted to have a deleterious effect on this acceptor splice site by BDGP; however, direct evidence is unavailable. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6499 samples (12998 alleles) with coverage at this position. To date, this alteration has been detected with an allele frequency of approximately 0.005% (greater than 22000 alleles tested) in our clinical cohort. This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of p.A823S remains unclear.

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

Last Updated: Sep 29, 2024