NM_000051.4(ATM):c.6415G>T (p.Glu2139Ter) AND Familial cancer of breast

Germline classification:: Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:: Jan 29, 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:: RCV003155959.10

Allele description [Variation Report for NM_000051.4(ATM):c.6415G>T (p.Glu2139Ter)]

NM_000051.4(ATM):c.6415G>T (p.Glu2139Ter)

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.6415G>T (p.Glu2139Ter)

HGVS:

NC_000011.10:g.108320021G>T
NG_009830.1:g.102190G>T
NG_054724.1:g.154812C>A
NM_000051.4:c.6415G>TMANE SELECT
NM_001330368.2:c.641-10950C>A
NM_001351110.2:c.*39-10950C>A
NM_001351834.2:c.6415G>T
NP_000042.3:p.Glu2139Ter
NP_000042.3:p.Glu2139Ter
NP_001338763.1:p.Glu2139Ter
LRG_135t1:c.6415G>T
LRG_135:g.102190G>T
LRG_135p1:p.Glu2139Ter
NC_000011.9:g.108190748G>T
NM_000051.3:c.6415G>T

Protein change:

E2139*

Links:

dbSNP: rs1339238483

NCBI 1000 Genomes Browser:

rs1339238483

Molecular consequence:

NM_001330368.2:c.641-10950C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001351110.2:c.*39-10950C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000051.4:c.6415G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001351834.2:c.6415G>T - nonsense - [Sequence Ontology: SO:0001587]

Observations:

Condition(s)

Name:: Familial cancer of breast
Synonyms:: Breast cancer, familial
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
SCV002588977	BRCAlab, Lund University	no assertion criteria provided	Pathogenic (Aug 26, 2022)	germline	clinical testing
SCV004212107	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jan 21, 2023)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004933166	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Pathogenic (Jan 29, 2024)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002588977

BRCAlab, Lund University

no assertion criteria provided

Pathogenic
(Aug 26, 2022)

germline

clinical testing

SCV004212107

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jan 21, 2023)

unknown

clinical testing

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

SCV004933166

Myriad Genetics, Inc.

criteria provided, single submitter

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

Pathogenic
(Jan 29, 2024)

unknown

clinical testing

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	1	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

Details of each submission

From BRCAlab, Lund University, SCV002588977.1

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

#	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	1	not provided

From Baylor Genetics, SCV004212107.1

#	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., SCV004933166.1

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

Description

This variant is considered pathogenic. This variant creates a termination codon and is predicted to result in premature protein truncation.

#	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: May 19, 2024

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