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NM_000051.4(ATM):c.2922-1G>T

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Interpretation:
Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: Jun 11, 2021)
Last evaluated:
May 18, 2020
Accession:
VCV000490499.6
Variation ID:
490499
Description:
single nucleotide variant
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NM_000051.4(ATM):c.2922-1G>T

Allele ID
484388
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11q22.3
Genomic location
11: 108141977 (GRCh37) GRCh37 UCSC
11: 108271250 (GRCh38) GRCh38 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000011.9:g.108141977G>T
LRG_135:g.53419G>T
LRG_135t1:c.2922-1G>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000011.10:108271249:G:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA382547064
dbSNP: rs1555084931
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 2 criteria provided, multiple submitters, no conflicts Jun 6, 2019 RCV000667991.3
Likely pathogenic 1 criteria provided, single submitter May 18, 2020 RCV000581238.4
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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
6418 10309

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Jun 29, 2017)
criteria provided, single submitter
Method: clinical testing
Ataxia-telangiectasia syndrome
Allele origin: unknown
Counsyl
Accession: SCV000792527.1
Submitted: (Jul 10, 2018)
Evidence details
Likely pathogenic
(May 18, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000687427.4
Submitted: (Jun 11, 2021)
Evidence details
Comment:
This variant causes a G to T nucleotide substitution at the -1 position of intron 19 of the ATM gene. Splice site prediction tools predict … (more)
Likely pathogenic
(Jun 06, 2019)
criteria provided, single submitter
Method: clinical testing
Ataxia-telangiectasia syndrome
Allele origin: germline
Invitae
Accession: SCV001394310.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change affects an acceptor splice site in intron 19 of the ATM gene. It is expected to disrupt RNA splicing and likely results … (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
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
Presence of ATM protein and residual kinase activity correlates with the phenotype in ataxia-telangiectasia: a genotype-phenotype study. Verhagen MM Human mutation 2012 PMID: 22213089
Splicing in action: assessing disease causing sequence changes. Baralle D Journal of medical genetics 2005 PMID: 16199547

Text-mined citations for rs1555084931...

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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 30, 2021