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NM_000051.4(ATM):c.901+3A>T AND Hereditary cancer-predisposing syndrome

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Nov 19, 2018
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000166211.6

Allele description [Variation Report for NM_000051.4(ATM):c.901+3A>T]

NM_000051.4(ATM):c.901+3A>T

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.901+3A>T
HGVS:
  • NC_000011.10:g.108245029A>T
  • NG_009830.1:g.27198A>T
  • NM_000051.4:c.901+3A>TMANE SELECT
  • NM_001351834.2:c.901+3A>T
  • LRG_135t1:c.901+3A>T
  • LRG_135:g.27198A>T
  • NC_000011.9:g.108115756A>T
  • NM_000051.3:c.901+3A>T
Links:
dbSNP: rs786203070
NCBI 1000 Genomes Browser:
rs786203070
Molecular consequence:
  • NM_000051.4:c.901+3A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001351834.2:c.901+3A>T - intron variant - [Sequence Ontology: SO:0001627]

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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000216990Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Uncertain significance
(Oct 19, 2014) 		germlineclinical testing

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

Citation Link,

SCV000913536Color Diagnostics, LLC DBA Color Health
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Nov 19, 2018) 		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

Characterization of ATM mutations in 41 Nordic families with ataxia telangiectasia.

Laake K, Jansen L, Hahnemann JM, Brondum-Nielsen K, Lönnqvist T, Kääriäinen H, Sankila R, Lähdesmäki A, Hammarström L, Yuen J, Tretli S, Heiberg A, Olsen JH, Tucker M, Kleinerman R, Børresen-Dale AL.

Hum Mutat. 2000 Sep;16(3):232-46.

PubMed [citation]
PMID:
10980530

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Ambry Genetics, SCV000216990.7

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

Description

The c.901+3A>T intronic variant results from an A to T substitution 3 nucleotides after coding exon 6 in the ATM gene. This alteration was detected in a single Swedish family affected with Ataxia Telagiectasia and was categorized as most likely disease causing due to predicted exon skipping (Laake K et al Hum Mutat. 2000 Sep;16(3):232-46). 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. To date, this alteration has been detected with an allele frequency of approximately 0.004% (greater than 22,000 alleles tested) in our clinical cohort. This nucleotide position is well conserved in available vertebrate species. In addition, this alteration is predicted to abolish the native donor site by the BDGP in silico model and significantly weaken the native donor site by the ESEfinder in silico model; however experimental evidence is not currently available. Since supporting evidence is limited at this time, the clinical significance of c.901+3A>T remains unclear.

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

From Color Diagnostics, LLC DBA Color Health, SCV000913536.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024