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NM_000051.4(ATM):c.4776+1G>T

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Aug 13, 2021)
Last evaluated:
Jul 6, 2020
Accession:
VCV000478920.7
Variation ID:
478920
Description:
single nucleotide variant
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NM_000051.4(ATM):c.4776+1G>T

Allele ID
476053
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11q22.3
Genomic location
11: 108293478 (GRCh38) GRCh38 UCSC
11: 108164205 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000011.10:g.108293478G>T
NC_000011.9:g.108164205G>T
NG_009830.1:g.75647G>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000011.10:108293477:G:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00001
Links
ClinGen: CA6265538
dbSNP: rs771117943
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 2 criteria provided, multiple submitters, no conflicts Feb 10, 2020 RCV000573615.6
Likely pathogenic 2 criteria provided, multiple submitters, no conflicts Mar 25, 2018 RCV000669160.2
Likely pathogenic 1 criteria provided, single submitter Jul 6, 2020 RCV001560132.2
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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

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Sep 12, 2017)
criteria provided, single submitter
Method: clinical testing
Ataxia-telangiectasia syndrome
Allele origin: unknown
Counsyl
Accession: SCV000793880.1
Submitted: (Jul 10, 2018)
Evidence details
Likely pathogenic
(Mar 25, 2018)
criteria provided, single submitter
Method: clinical testing
Ataxia-telangiectasia syndrome
Allele origin: germline
Invitae
Accession: SCV000823408.1
Submitted: (Aug 29, 2018)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change affects a donor splice site in intron 31 of the ATM gene. It is expected to disrupt RNA splicing and likely results … (more)
Likely pathogenic
(Mar 18, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000687567.3
Submitted: (May 19, 2020)
Evidence details
Pathogenic
(Feb 10, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000660445.3
Submitted: (Nov 30, 2020)
Evidence details
Publications
PubMed (2)
Comment:
The c.4776+1G>T intronic pathogenic mutation results from a G to T substitution one nucleotide after coding exon 30 of the ATM gene. This nucleotide position … (more)
Likely pathogenic
(Jul 06, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001782480.1
Submitted: (Aug 13, 2021)
Evidence details
Comment:
Canonical splice site variant demonstrated to result in an in-frame deletion of exon 31 (Fivet 2019); Observed in an individual with familial breast cancer; however, … (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
Functional classification of ATM variants in ataxia-telangiectasia patients. Fiévet A Human mutation 2019 PMID: 31050087
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
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
Efficacy of very-low-dose betamethasone on neurological symptoms in ataxia-telangiectasia. Broccoletti T European journal of neurology 2011 PMID: 20840352

Text-mined citations for rs771117943...

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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 27, 2021