NM_000051.4(ATM):c.7789-3T>G AND Familial cancer of breast

Germline classification:: Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:: Feb 1, 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:: RCV001310118.11

Allele description [Variation Report for NM_000051.4(ATM):c.7789-3T>G]

NM_000051.4(ATM):c.7789-3T>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.7789-3T>G

HGVS:

NC_000011.10:g.108332759T>G
NG_009830.1:g.114928T>G
NG_054724.1:g.142074A>C
NM_000051.4:c.7789-3T>GMANE SELECT
NM_001330368.2:c.641-23688A>C
NM_001351110.2:c.*38+2461A>C
NM_001351834.2:c.7789-3T>G
LRG_135t1:c.7789-3T>G
LRG_135:g.114928T>G
NC_000011.9:g.108203486T>G
NM_000051.3:c.7789-3T>G

Links:

dbSNP: rs864622185

NCBI 1000 Genomes Browser:

rs864622185

Molecular consequence:

NM_000051.4:c.7789-3T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001330368.2:c.641-23688A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001351110.2:c.*38+2461A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001351834.2:c.7789-3T>G - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Familial cancer of breast
Synonyms:: Breast cancer, familial; Hereditary breast cancer
Identifiers:: MONDO: MONDO:0016419; MedGen: C0346153; OMIM: 114480

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001499660	Department of Molecular Diagnostics, Institute of Oncology Ljubljana	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Apr 2, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004216244	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jan 28, 2021)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004932246	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Likely pathogenic (Feb 1, 2024)	unknown	clinical testing	PubMed (4) [See all records that cite these PMIDs] 8808599, 12815592, 17124347, 21965147 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001499660

Department of Molecular Diagnostics, Institute of Oncology Ljubljana

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Apr 2, 2020)

germline

clinical testing

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

SCV004216244

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jan 28, 2021)

unknown

clinical testing

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

SCV004932246

Myriad Genetics, Inc.

criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))

Likely pathogenic
(Feb 1, 2024)

unknown

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	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

A high frequency of distinct ATM gene mutations in ataxia-telangiectasia.

Wright J, Teraoka S, Onengut S, Tolun A, Gatti RA, Ochs HD, Concannon P.

Am J Hum Genet. 1996 Oct;59(4):839-46.

PubMed [citation]

PMID:: 8808599
PMCID:: PMC1914811

See all PubMed Citations (5)

Details of each submission

From Department of Molecular Diagnostics, Institute of Oncology Ljubljana, SCV001499660.1

#	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	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Baylor Genetics, SCV004216244.1

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Myriad Genetics, Inc., SCV004932246.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This variant is considered likely pathogenic. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 8808599, 12815592, 17124347, 21965147].

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 3, 2024

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