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NM_000051.4(ATM):c.3919G>A (p.Gly1307Arg)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(2);Likely benign(3);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
7 (Most recent: Sep 24, 2021)
Last evaluated:
Dec 6, 2020
Accession:
VCV000142243.11
Variation ID:
142243
Description:
single nucleotide variant
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NM_000051.4(ATM):c.3919G>A (p.Gly1307Arg)

Allele ID
151957
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11q22.3
Genomic location
11: 108284399 (GRCh38) GRCh38 UCSC
11: 108155126 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_135:g.66568G>A
LRG_135t1:c.3919G>A LRG_135p1:p.Gly1307Arg
NC_000011.9:g.108155126G>A
... more HGVS
Protein change
G1307R
Other names
-
Canonical SPDI
NC_000011.10:108284398:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00080 (A)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00002
The Genome Aggregation Database (gnomAD), exomes 0.00036
Exome Aggregation Consortium (ExAC) 0.00043
The Genome Aggregation Database (gnomAD) 0.00003
The Genome Aggregation Database (gnomAD) 0.00000
1000 Genomes Project 0.00080
Links
ClinGen: CA167867
dbSNP: rs568451087
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 Feb 22, 2019 RCV000131248.7
Likely benign 1 criteria provided, single submitter Sep 14, 2020 RCV000608362.2
Likely benign 1 criteria provided, single submitter Nov 27, 2020 RCV001704057.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Dec 6, 2020 RCV000234723.8
Likely benign 1 no assertion criteria provided - RCV001356054.1
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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
(Feb 22, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000186209.6
Submitted: (Nov 30, 2020)
Evidence details
Comment:
In silico models in agreement (benign);Other strong data supporting benign classification
Benign
(Dec 06, 2020)
criteria provided, single submitter
Method: clinical testing
Ataxia-telangiectasia syndrome
Allele origin: germline
Invitae
Accession: SCV000282946.7
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Oct 06, 2016)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000910688.1
Submitted: (Nov 06, 2018)
Evidence details
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Ataxia-telangiectasia syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001260528.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Likely benign
(Sep 14, 2020)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001437333.1
Submitted: (Oct 06, 2020)
Evidence details
Publications
PubMed (4)
Comment:
Variant summary: ATM c.3919G>A (p.Gly1307Arg) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign … (more)
Likely benign
(Nov 27, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000729394.1
Submitted: (Sep 24, 2021)
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: SCV001551112.1
Submitted: (Mar 31, 2021)
Evidence details
Comment:
The ATM p.Gly1307Arg variant was not identified in the literature nor was it identified in the GeneInsight-COGR, Cosmic, or MutDB databases. The variant was identified … (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
Germline mutations in candidate predisposition genes in individuals with cutaneous melanoma and at least two independent additional primary cancers. Pritchard AL PloS one 2018 PMID: 29641532
Mutation Detection in Patients With Advanced Cancer by Universal Sequencing of Cancer-Related Genes in Tumor and Normal DNA vs Guideline-Based Germline Testing. Mandelker D JAMA 2017 PMID: 28873162
Patterns and functional implications of rare germline variants across 12 cancer types. Lu C Nature communications 2015 PMID: 26689913
Heterozygosity for mutations in the ataxia telangiectasia gene is not a major cause of radiotherapy complications in breast cancer patients. Shayeghi M British journal of cancer 1998 PMID: 9764584

Text-mined citations for rs568451087...

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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