NM_000051.4(ATM):c.7089+3A>G AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Apr 16, 2024
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:: RCV001183564.13

Allele description [Variation Report for NM_000051.4(ATM):c.7089+3A>G]

NM_000051.4(ATM):c.7089+3A>G

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+3A>G

HGVS:

NC_000011.10:g.108327761A>G
NG_009830.1:g.109930A>G
NG_054724.1:g.147072T>C
NM_000051.4:c.7089+3A>GMANE SELECT
NM_001330368.2:c.641-18690T>C
NM_001351110.2:c.*38+7459T>C
NM_001351834.2:c.7089+3A>G
LRG_135t1:c.7089+3A>G
LRG_135:g.109930A>G
NC_000011.9:g.108198488A>G
NM_000051.3:c.7089+3A>G

Links:

dbSNP: rs1565524203

NCBI 1000 Genomes Browser:

rs1565524203

Molecular consequence:

NM_000051.4:c.7089+3A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001330368.2:c.641-18690T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001351110.2:c.*38+7459T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001351834.2:c.7089+3A>G - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001349354	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Dec 5, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002662560	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Apr 16, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001349354

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Dec 5, 2018)

germline

clinical testing

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

SCV002662560

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Apr 16, 2024)

germline

clinical testing

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

Citation Link

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

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

Pathogenic Germline Variants in Patients With Metastatic Breast Cancer.

Stuttgen K, Croessmann S, Fetting J, Stearns V, Nunes R, Connolly RM, Park BH.

JAMA Oncol. 2019 Oct 1;5(10):1506-1508. doi: 10.1001/jamaoncol.2019.3116. No abstract available.

PubMed [citation]

PMID:: 31465090
PMCID:: PMC6802240

Details of each submission

From Color Diagnostics, LLC DBA Color Health, SCV001349354.1

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

#	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

From Ambry Genetics, SCV002662560.3

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

Description

The c.7089+3A>G intronic variant results from an A to G substitution 3 nucleotides after coding exon 47 in the ATM gene. This variant was identified in a cohort of individuals diagnosed with metastatic breast cancer who underwent germline testing of 30 genes (Stuttgen K et al. JAMA Oncol, 2019 Oct;5:1506-1508). This nucleotide position is well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will not have any significant effect on splicing. Based on the available evidence, the clinical significance of this variant remains unclear.

#	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: Oct 8, 2024

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