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NM_000051.4(ATM):c.7089+1G>A AND Hereditary cancer-predisposing syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jan 25, 2016
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:
RCV000571077.11

Allele description [Variation Report for NM_000051.4(ATM):c.7089+1G>A]

NM_000051.4(ATM):c.7089+1G>A

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.7089+1G>A
HGVS:
  • NC_000011.10:g.108327759G>A
  • NG_009830.1:g.109928G>A
  • NG_054724.1:g.147074C>T
  • NM_000051.4:c.7089+1G>AMANE SELECT
  • NM_001330368.2:c.641-18688C>T
  • NM_001351110.2:c.*38+7461C>T
  • NM_001351834.2:c.7089+1G>A
  • LRG_135t1:c.7089+1G>A
  • LRG_135:g.109928G>A
  • NC_000011.9:g.108198486G>A
  • NM_000051.3:c.7089+1G>A
Links:
dbSNP: rs777741666
NCBI 1000 Genomes Browser:
rs777741666
Molecular consequence:
  • NM_001330368.2:c.641-18688C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001351110.2:c.*38+7461C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000051.4:c.7089+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001351834.2:c.7089+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
SCV000672636Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely pathogenic
(Jan 25, 2016) 		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, SCV000672636.5

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

Description

The c.7089+1G>A intronic variant results from a G to A substitution one nucleotide after coding exon 47 of the ATM gene. 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 0.001% (greater than 125000 alleles tested) in our clinical cohort. This nucleotide position is highly conserved in available vertebrate species. Using the BDGP and ESEfinder splice site prediction tools, this alteration is predicted to abolish the native splice donor site; however, direct evidence is unavailable. Alterations that disrupt the canonical splice donor site are typically deleterious in nature (ACMG Recommendations for Standards for Interpretation and Reporting of Sequence Variations. Revision 2007. Genet Med. 2008;10:294). As such, the c.7089+1G>A variant is classified as likely pathogenic.

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

Last Updated: Nov 10, 2024