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NM_000051.4(ATM):c.2921+1G>C

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
7 (Most recent: Nov 19, 2021)
Last evaluated:
Jul 14, 2020
Accession:
VCV000188097.11
Variation ID:
188097
Description:
single nucleotide variant
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NM_000051.4(ATM):c.2921+1G>C

Allele ID
186142
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11q22.3
Genomic location
11: 108271147 (GRCh38) GRCh38 UCSC
11: 108141874 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000011.9:g.108141874G>C
LRG_135:g.53316G>C
LRG_135t1:c.2921+1G>C
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000011.10:108271146:G:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA334038
dbSNP: rs587781558
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 Jul 14, 2020 RCV000167947.7
Pathogenic/Likely pathogenic 3 criteria provided, multiple submitters, no conflicts Oct 1, 2019 RCV000217319.7
Pathogenic 1 criteria provided, single submitter Nov 21, 2016 RCV000236109.2
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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
(Aug 15, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000682088.3
Submitted: (May 19, 2020)
Comment:
This variant causes a G>C nucleotide substitution at the +1 position of intron 19 of the ATM gene. Splice site prediction tools suggest that this … (more)
Evidence details
Likely pathogenic
(Nov 08, 2017)
criteria provided, single submitter
Method: clinical testing
Ataxia-telangiectasia syndrome
Allele origin: unknown
Counsyl
Accession: SCV000795509.1
Submitted: (Jul 10, 2018)
Evidence details
Pathogenic
(Jul 14, 2020)
criteria provided, single submitter
Method: clinical testing
Ataxia-telangiectasia syndrome
Allele origin: germline
Invitae
Accession: SCV000218595.7
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change affects a donor splice site in intron 19 of the ATM gene. It is expected to disrupt RNA splicing and likely results … (more)
Pathogenic
(Nov 21, 2016)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000293826.10
Submitted: (Jan 29, 2019)
Evidence details
Comment:
This variant is denoted ATM c.2921+1G>C or IVS19+1G>C and consists of a G>C nucleotide substitution at the +1 position of intron 19 of the ATM … (more)
Pathogenic
(Oct 01, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000277701.6
Submitted: (Nov 30, 2020)
Evidence details
Publications
PubMed (3)
Comment:
The c.2921+1G>C intronic pathogenic mutation results from a G to C substitution one nucleotide after coding exon 18 of the ATM gene. A similar alteration, … (more)
Pathogenic
(-)
criteria provided, single submitter
Method: research
Hereditary cancer-predisposing syndrome
Allele origin: inherited
Department of Pediatric Oncology, Hematology and Clinical Immunology,University Clinics Duesseldorf
Accession: SCV001482291.1
Submitted: (Feb 23, 2021)
Evidence details
Pathogenic
(Feb 01, 2019)
no assertion criteria provided
Method: clinical testing
Ataxia-telangiectasia syndrome
Allele origin: germline
PerkinElmer Genomics
Accession: SCV002021918.1
Submitted: (Nov 19, 2021)
Evidence details

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
RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease. Xiong HY Science (New York, N.Y.) 2015 PMID: 25525159
Molecular defects in Moroccan patients with ataxia-telangiectasia. Jeddane L Neuromolecular medicine 2013 PMID: 23322442
Independent mutational events are rare in the ATM gene: haplotype prescreening enhances mutation detection rate. Mitui M Human mutation 2003 PMID: 12815592
Novel mutations and defective protein kinase C activation of T-lymphocytes in ataxia telangiectasia. García-Pérez MA Clinical and experimental immunology 2001 PMID: 11298136
Predominance of null mutations in ataxia-telangiectasia. Gilad S Human molecular genetics 1996 PMID: 8845835

Text-mined citations for rs587781558...

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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 28, 2021