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NM_000051.4(ATM):c.2630G>C (p.Ser877Thr)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(2);Likely benign(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
8 (Most recent: Oct 15, 2021)
Last evaluated:
Dec 7, 2020
Accession:
VCV000127356.12
Variation ID:
127356
Description:
single nucleotide variant
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NM_000051.4(ATM):c.2630G>C (p.Ser877Thr)

Allele ID
132813
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11q22.3
Genomic location
11: 108267334 (GRCh38) GRCh38 UCSC
11: 108138061 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000011.10:g.108267334G>C
NG_009830.1:g.49503G>C
NM_000051.4:c.2630G>C MANE Select NP_000042.3:p.Ser877Thr missense
... more HGVS
Protein change
S877T
Other names
p.S877T:AGT>ACT
Canonical SPDI
NC_000011.10:108267333:G:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00001
Exome Aggregation Consortium (ExAC) 0.00005
Trans-Omics for Precision Medicine (TOPMed) 0.00002
The Genome Aggregation Database (gnomAD), exomes 0.00004
Links
ClinGen: CA286772
dbSNP: rs370269552
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Mar 30, 2018 RCV000115161.10
Likely benign 4 criteria provided, single submitter Mar 8, 2019 RCV000211985.8
Benign 1 criteria provided, single submitter Dec 7, 2020 RCV001083203.2
Uncertain significance 1 criteria provided, single submitter Jan 10, 2020 RCV001174578.1
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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
6424 10317

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Mar 30, 2018)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000184961.6
Submitted: (Nov 30, 2020)
Evidence details
Comment:
Co-occurence with mutation in same gene (phase unknown);in silico models in agreement (benign)
Benign
(Dec 07, 2020)
criteria provided, single submitter
Method: clinical testing
Ataxia-telangiectasia syndrome
Allele origin: germline
Invitae
Accession: SCV000219104.11
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Likely benign
(Mar 08, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000149070.14
Submitted: (Sep 25, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 19781682, 26689913, 30093976)
Benign
(Sep 09, 2015)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000910866.1
Submitted: (Nov 06, 2018)
Evidence details
Uncertain significance
(Jan 10, 2020)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001337756.1
Submitted: (Apr 29, 2020)
Evidence details
Publications
PubMed (5)
Comment:
Variant summary: ATM c.2630G>C (p.Ser877Thr) results in a conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a benign … (more)
Uncertain significance
(-)
no assertion criteria provided
Method: clinical testing
not provided
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: SCV001548706.1
Submitted: (Mar 31, 2021)
Evidence details
Comment:
The ATM p.Ser877Thr variant was identified in 3 of 5062 proband chromosomes (frequency: 0.0006) from individuals or families with breast cancer and was present in … (more)
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Genome Diagnostics Laboratory, Amsterdam University Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001977657.1
Submitted: (Oct 15, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Human Genetics - Radboudumc,Radboudumc
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001979393.1
Submitted: (Oct 15, 2021)
Evidence details

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
Clinical genetic testing outcome with multi-gene panel in Asian patients with multiple primary cancers. Chan GHJ Oncotarget 2018 PMID: 30093976
Germline Mutations in DNA Repair Genes in Lung Adenocarcinoma. Parry EM Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer 2017 PMID: 28843361
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
Patterns and functional implications of rare germline variants across 12 cancer types. Lu C Nature communications 2015 PMID: 26689913
Radiation exposure, the ATM Gene, and contralateral breast cancer in the women's environmental cancer and radiation epidemiology study. Bernstein JL Journal of the National Cancer Institute 2010 PMID: 20305132
Rare, evolutionarily unlikely missense substitutions in ATM confer increased risk of breast cancer. Tavtigian SV American journal of human genetics 2009 PMID: 19781682

Text-mined citations for rs370269552...

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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 Dec 04, 2021