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NM_000051.4(ATM):c.8786+1G>T

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Sep 14, 2021)
Last evaluated:
Jun 17, 2020
Accession:
VCV000184741.9
Variation ID:
184741
Description:
single nucleotide variant
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NM_000051.4(ATM):c.8786+1G>T

Allele ID
183456
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11q22.3
Genomic location
11: 108353881 (GRCh38) GRCh38 UCSC
11: 108224608 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000011.9:g.108224608G>T
LRG_135:g.136050G>T
LRG_135t1:c.8786+1G>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000011.10:108353880:G:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00001
The Genome Aggregation Database (gnomAD) 0.00001
Links
ClinGen: CA189911
dbSNP: rs17174393
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 3 criteria provided, multiple submitters, no conflicts Jun 17, 2020 RCV000164050.6
Pathogenic/Likely pathogenic 2 criteria provided, multiple submitters, no conflicts Dec 16, 2019 RCV000540315.5
Pathogenic 1 criteria provided, single submitter Apr 30, 2019 RCV001558979.2
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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
C11orf65 - - - GRCh38
GRCh37
3 3892

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Nov 15, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000214657.6
Submitted: (Nov 30, 2020)
Evidence details
Comment:
The c.8786+1G>T intronic pathogenic mutation results from a G to T substitution one nucleotide after coding exon 59 of the ATM gene. To our knowledge, … (more)
Likely pathogenic
(Jul 17, 2017)
criteria provided, single submitter
Method: clinical testing
Ataxia-telangiectasia syndrome
Allele origin: unknown
Counsyl
Accession: SCV000792812.1
Submitted: (Jul 10, 2018)
Evidence details
Likely pathogenic
(Nov 26, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV001353288.1
Submitted: (May 19, 2020)
Comment:
This variant causes a G>T nucleotide substitution at the +1 position of intron 60 of the ATM gene. Splice site prediction tools predict that this … (more)
Evidence details
Pathogenic
(Dec 16, 2019)
criteria provided, single submitter
Method: clinical testing
Ataxia-telangiectasia syndrome
Allele origin: germline
Invitae
Accession: SCV000622851.5
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (13)
Comment:
This sequence change affects a donor splice site in intron 60 of the ATM gene. It is expected to disrupt RNA splicing and likely results … (more)
Pathogenic
(Apr 30, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001781030.1
Submitted: (Aug 10, 2021)
Evidence details
Comment:
Canonical splice site variant in a gene for which loss-of-function is a known mechanism of disease; Not observed in large population cohorts (Lek et al., … (more)
Pathogenic
(Jun 17, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Spanish ATM Cancer Susceptibility Variant Interpretation Working Group
Accession: SCV001911491.1
Submitted: (Sep 14, 2021)
Evidence details
Publications
PubMed (1)
Comment:
The c.8786+1G>T variant is located in the canonical donor splice site of intron 60 and it is predicted to cause the skipping of exon 60 … (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
A Collaborative Effort to Define Classification Criteria for ATM Variants in Hereditary Cancer Patients. Feliubadaló L Clinical chemistry 2021 PMID: 33280026
Ten new ATM alterations in Polish patients with ataxia-telangiectasia. Podralska MJ Molecular genetics & genomic medicine 2014 PMID: 25614872
Twelve novel Atm mutations identified in Chinese ataxia telangiectasia patients. Huang Y Neuromolecular medicine 2013 PMID: 23807571
Lymphoid tumours and breast cancer in ataxia telangiectasia; substantial protective effect of residual ATM kinase activity against childhood tumours. Reiman A British journal of cancer 2011 PMID: 21792198
Premature ageing of the immune system underlies immunodeficiency in ataxia telangiectasia. Exley AR Clinical immunology (Orlando, Fla.) 2011 PMID: 21459046
Germline ATM mutational analysis in BRCA1/BRCA2 negative hereditary breast cancer families by MALDI-TOF mass spectrometry. Graña B Breast cancer research and treatment 2011 PMID: 21445571
Splicing in action: assessing disease causing sequence changes. Baralle D Journal of medical genetics 2005 PMID: 16199547
Novel mutations and defective protein kinase C activation of T-lymphocytes in ataxia telangiectasia. García-Pérez MA Clinical and experimental immunology 2001 PMID: 11298136
Characterization of ATM mutations in 41 Nordic families with ataxia telangiectasia. Laake K Human mutation 2000 PMID: 10980530
Mutations at the ataxia-telangiectasia locus and clinical phenotypes of A-T patients. Li A American journal of medical genetics 2000 PMID: 10817650
Splicing defects in the ataxia-telangiectasia gene, ATM: underlying mutations and consequences. Teraoka SN American journal of human genetics 1999 PMID: 10330348
ATM mutations and phenotypes in ataxia-telangiectasia families in the British Isles: expression of mutant ATM and the risk of leukemia, lymphoma, and breast cancer. Stankovic T American journal of human genetics 1998 PMID: 9463314
A high frequency of distinct ATM gene mutations in ataxia-telangiectasia. Wright J American journal of human genetics 1996 PMID: 8808599
Ataxia-telangiectasia: mutations in ATM cDNA detected by protein-truncation screening. Telatar M American journal of human genetics 1996 PMID: 8659541

Text-mined citations for rs17174393...

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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