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NM_000051.3(ATM):c.2614C>T (p.Pro872Ser)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
19 (Most recent: Oct 15, 2021)
Last evaluated:
Dec 2, 2020
Accession:
VCV000133610.17
Variation ID:
133610
Description:
single nucleotide variant
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NM_000051.3(ATM):c.2614C>T (p.Pro872Ser)

Allele ID
137349
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11q22.3
Genomic location
11: 108267318 (GRCh38) GRCh38 UCSC
11: 108138045 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
Q13315:p.Pro872Ser
NC_000011.10:g.108267318C>T
NC_000011.9:g.108138045C>T
... more HGVS
Protein change
P872S
Other names
p.P872S:CCT>TCT
Canonical SPDI
NC_000011.10:108267317:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.01637 (T)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.01170
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.01600
Trans-Omics for Precision Medicine (TOPMed) 0.01437
1000 Genomes Project 0.01637
Links
ClinGen: CA157083
UniProtKB: Q13315#VAR_041557
dbSNP: rs3218673
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 9 criteria provided, multiple submitters, no conflicts Oct 21, 2016 RCV000120126.7
Benign 3 criteria provided, multiple submitters, no conflicts Nov 25, 2014 RCV000128879.5
Benign 2 criteria provided, multiple submitters, no conflicts May 30, 2018 RCV000224090.4
Benign/Likely benign 3 criteria provided, multiple submitters, no conflicts Dec 2, 2020 RCV000204457.10
Benign 1 criteria provided, single submitter Jun 5, 2020 RCV001289746.1
Benign 1 no assertion criteria provided - RCV001354699.1
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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
6396 10264

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Dec 22, 2015)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000281433.1
Submitted: (May 19, 2016)
Evidence details
Benign
(Nov 05, 2014)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000682065.1
Submitted: (Oct 26, 2017)
Evidence details
Benign
(Oct 01, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000167074.11
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)
Benign
(Oct 21, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000805522.1
Submitted: (Jan 29, 2018)
Evidence details
Benign
(May 30, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000840929.1
Submitted: (Aug 31, 2018)
Evidence details
Benign
(Feb 16, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000226548.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Ataxia-telangiectasia syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000367037.3
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (2)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Benign
(Dec 02, 2020)
criteria provided, single submitter
Method: clinical testing
Ataxia-telangiectasia syndrome
Allele origin: germline
Invitae
Accession: SCV000262431.8
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Nov 25, 2014)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000172736.7
Submitted: (Nov 30, 2020)
Evidence details
Comment:
This alteration is classified as benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA … (more)
Benign
(Jun 05, 2020)
criteria provided, single submitter
Method: clinical testing
none provided
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories
Accession: SCV001477728.1
Submitted: (Dec 11, 2020)
Evidence details
Likely benign
(Jun 18, 2018)
no assertion criteria provided
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
True Health Diagnostics
Accession: SCV000805214.1
Submitted: (Jun 26, 2018)
Evidence details
Benign
(Apr 17, 2020)
no assertion criteria provided
Method: clinical testing
Ataxia-telangiectasia
Allele origin: germline
Natera, Inc.
Accession: SCV001461093.1
Submitted: (Dec 28, 2020)
Evidence details
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: SCV001549380.1
Submitted: (Mar 31, 2021)
Evidence details
Comment:
The ATM p.Pro872Ser variant was identified in 10 of 1192 proband chromosomes (frequency: 0.008) from individuals or families with breast cancer, multiple myeloma and from … (more)
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001740465.3
Submitted: (Sep 02, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Clinical Genetics Laboratory, Department of Pathology,Netherlands Cancer Institute
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001906188.1
Submitted: (Sep 20, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Clinical Genetics,Academic Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001920784.1
Submitted: (Sep 23, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Human Genetics - Radboudumc,Radboudumc
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001951509.1
Submitted: (Sep 30, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Genome Diagnostics Laboratory, University Medical Center Utrecht
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001977987.1
Submitted: (Oct 15, 2021)
Evidence details
not provided
(Sep 19, 2013)
no assertion provided
Method: reference population
AllHighlyPenetrant
Allele origin: germline
ITMI
Accession: SCV000084264.1
Submitted: (May 29, 2014)
Comment:
Please see associated publication for description of ethnicities
Evidence details
Publications
PubMed (1)

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
Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing. Bodian DL PloS one 2014 PMID: 24728327
Pathogenic ATM mutations occur rarely in a subset of multiple myeloma patients. Austen B British journal of haematology 2008 PMID: 18573109
Elevated frequency of ATM gene missense mutations in breast cancer relative to ethnically matched controls. Sommer SS Cancer genetics and cytogenetics 2002 PMID: 11996792
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=ATM - - - -

Text-mined citations for rs3218673...

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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 Oct 16, 2021