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NM_000051.4(ATM):c.3449G>C (p.Arg1150Thr)

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Interpretation:
Conflicting interpretations of pathogenicity​

Uncertain significance(3); Likely benign(5)

Review status:
criteria provided, conflicting interpretations
Submissions:
9
First in ClinVar:
Jul 24, 2016
Most recent Submission:
Nov 29, 2022
Last evaluated:
May 27, 2022
Accession:
VCV000127372.24
Variation ID:
127372
Description:
single nucleotide variant
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NM_000051.4(ATM):c.3449G>C (p.Arg1150Thr)

Allele ID
132829
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11q22.3
Genomic location
11: 108281041 (GRCh38) GRCh38 UCSC
11: 108151768 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_000051.4:c.3449G>C MANE Select NP_000042.3:p.Arg1150Thr missense
NM_001351834.2:c.3449G>C NP_001338763.1:p.Arg1150Thr missense
NC_000011.10:g.108281041G>C
... more HGVS
Protein change
R1150T
Other names
p.R1150T:AGA>ACA
Canonical SPDI
NC_000011.10:108281040:G:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.00060 (C)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00001
The Genome Aggregation Database (gnomAD), exomes 0.00018
Exome Aggregation Consortium (ExAC) 0.00019
1000 Genomes Project 0.00060
Links
ClinGen: CA286809
dbSNP: rs555219189
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Apr 8, 2021 RCV000115177.7
Likely benign 3 criteria provided, multiple submitters, no conflicts Dec 5, 2021 RCV000215488.10
Likely benign 2 criteria provided, single submitter Dec 13, 2021 RCV000199179.13
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations May 27, 2022 RCV001818259.4
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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
8326 13383

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter More information
Uncertain significance
(Mar 10, 2020)
criteria provided, single submitter
Method: clinical testing
Not provided
Affected status: unknown
Allele origin: germline
Mayo Clinic Laboratories,Mayo Clinic
Accession: SCV001714396.1
First in ClinVar: Jun 15, 2021
Last updated: Jun 15, 2021
Number of individuals with the variant: 1
Uncertain significance
(Apr 08, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Affected status: yes
Allele origin: germline
GeneDx
Accession: SCV000149086.13
First in ClinVar: May 17, 2014
Last updated: Jul 24, 2016
Comment:
In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Observed in individuals with breast or ovarian cancer (Singh 2018); … (more)
Uncertain significance
(Mar 02, 2018)
criteria provided, single submitter
Method: clinical testing
not specified
Affected status: no
Allele origin: germline
Genetic Services Laboratory,University of Chicago
Accession: SCV002068402.1
First in ClinVar: Jan 29, 2022
Last updated: Jan 29, 2022
Likely benign
(Dec 13, 2021)
criteria provided, single submitter
Method: clinical testing
Ataxia-telangiectasia syndrome
Affected status: unknown
Allele origin: germline
Invitae
Accession: SCV000254084.9
First in ClinVar: Oct 11, 2015
Last updated: May 16, 2022
Publications:
PubMed (1)
PubMed: 28492532
Likely benign
(Dec 05, 2021)
criteria provided, single submitter
Method: curation
Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin: germline
Sema4,Sema4
Accession: SCV002536023.1
First in ClinVar: Jun 24, 2022
Last updated: Jun 24, 2022
Publications:
PubMed (3)
PubMed: 294708063355295233471991
Likely benign
(May 27, 2022)
criteria provided, single submitter
Method: clinical testing
not specified
Affected status: unknown
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV002548067.1
First in ClinVar: Jul 18, 2022
Last updated: Jul 18, 2022
Publications:
PubMed (1)
PubMed: 29470806
Comment:
Variant summary: ATM c.3449G>C (p.Arg1150Thr) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging … (more)
Likely benign
(Apr 20, 2021)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin: germline
Ambry Genetics
Accession: SCV000278041.6
First in ClinVar: May 29, 2016
Last updated: Nov 29, 2022
Publications:
PubMed (4)
PubMed: 28580595294708063174282433471991
Comment:
This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, … (more)
Number of individuals with the variant: 1
Likely benign
(Oct 20, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin: germline
Color Diagnostics, LLC DBA Color Health
Accession: SCV000687480.4
First in ClinVar: Feb 19, 2018
Last updated: Jun 19, 2021
Uncertain significance
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Ataxia-telangiectasia
Affected status: unknown
Allele origin: germline
Natera, Inc.
Accession: SCV001457147.1
First in ClinVar: Jan 02, 2021
Last updated: Jan 02, 2021

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
Mutational Landscape for Indian Hereditary Breast and Ovarian Cancer Cohort Suggests Need for Identifying Population Specific Genes and Biomarkers for Screening. Kadri MSN Frontiers in oncology 2021 PMID: 33552952
Breast Cancer Risk Genes - Association Analysis in More than 113,000 Women. Breast Cancer Association Consortium The New England journal of medicine 2021 PMID: 33471991
Prevalence of hereditary breast and ovarian cancer (HBOC) predisposition gene mutations among 882 HBOC high-risk Chinese individuals. Shao D Cancer science 2020 PMID: 31742824
Screening of over 1000 Indian patients with breast and/or ovarian cancer with a multi-gene panel: prevalence of BRCA1/2 and non-BRCA mutations. Singh J Breast cancer research and treatment 2018 PMID: 29470806
Mutation screening of 10 cancer susceptibility genes in unselected breast cancer patients. Xie Y Clinical genetics 2018 PMID: 28580595
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532

Text-mined citations for rs555219189...

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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 29, 2022