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NM_000051.4(ATM):c.3154-4G>A

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(2);Likely benign(3);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
9 (Most recent: Nov 4, 2021)
Last evaluated:
Nov 3, 2021
Accession:
VCV000142254.16
Variation ID:
142254
Description:
single nucleotide variant
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NM_000051.4(ATM):c.3154-4G>A

Allele ID
151968
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11q22.3
Genomic location
11: 108272718 (GRCh38) GRCh38 UCSC
11: 108143445 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_135:g.54887G>A
LRG_135t1:c.3154-4G>A
NM_000051.3:c.3154-4G>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000011.10:108272717:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (A)

Allele frequency
1000 Genomes Project 0.00020
Trans-Omics for Precision Medicine (TOPMed) 0.00013
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00023
Links
ClinGen: CA294338
dbSNP: rs199543313
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 2 criteria provided, multiple submitters, no conflicts Sep 27, 2018 RCV000131267.7
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Jul 28, 2017 RCV000588159.5
Benign 1 criteria provided, single submitter Aug 7, 2014 RCV000211993.1
Benign 2 criteria provided, single submitter Dec 8, 2020 RCV001079697.3
Likely benign 1 criteria provided, single submitter Nov 3, 2021 RCV001762308.1
Likely benign 1 no assertion criteria provided - RCV001358310.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ATM Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
6418 10309

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Aug 07, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000209596.10
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Uncertain significance
(Jul 28, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000694250.1
Submitted: (Jan 25, 2018)
Evidence details
Publications
PubMed (2)
Likely benign
(Sep 27, 2018)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000186235.6
Submitted: (Nov 30, 2020)
Evidence details
Comment:
In silico models in agreement (benign);Other strong data supporting benign classification
Benign
(Dec 08, 2020)
criteria provided, single submitter
Method: clinical testing
Ataxia-telangiectasia syndrome
Allele origin: germline
Invitae
Accession: SCV000252955.9
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Nov 03, 2021)
criteria provided, single submitter
Method: clinical testing
Familial cancer of breast
Allele origin: germline
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden
Accession: SCV002010833.1
Submitted: (Nov 04, 2021)
Evidence details
Likely benign
(Dec 10, 2015)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000537432.1
Submitted: (Jan 26, 2017)
Evidence details
Uncertain significance
(Apr 01, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001148413.7
Submitted: (Jul 04, 2021)
Evidence details
Uncertain significance
(Jan 10, 2020)
no assertion criteria provided
Method: clinical testing
Ataxia-telangiectasia
Allele origin: germline
Natera, Inc.
Accession: SCV001462133.1
Submitted: (Dec 28, 2020)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
Malignant tumor of breast
Allele origin: unknown
Department of Pathology and Laboratory Medicine,Sinai Health System
Additional submitter:
Franklin by Genoox
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV001554010.1
Submitted: (Mar 31, 2021)
Evidence details
Comment:
The ATM c.3154-4G>A variant was identified in 2 of 3100 proband chromosomes (frequency: 0.0006) from individuals or families with Lynch Syndrome and pancreatic cancer (Yurgelun … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Identification of a Variety of Mutations in Cancer Predisposition Genes in Patients With Suspected Lynch Syndrome. Yurgelun MB Gastroenterology 2015 PMID: 25980754
Prevalence of germline mutations in cancer predisposition genes in patients with pancreatic cancer. Grant RC Gastroenterology 2015 PMID: 25479140

Text-mined citations for rs199543313...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 06, 2021