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NM_001184.4(ATR):c.891G>C (p.Lys297Asn)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
8 (Most recent: Sep 2, 2021)
Last evaluated:
Dec 8, 2020
Accession:
VCV000158005.9
Variation ID:
158005
Description:
single nucleotide variant
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NM_001184.4(ATR):c.891G>C (p.Lys297Asn)

Allele ID
167852
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
3q23
Genomic location
3: 142562511 (GRCh38) GRCh38 UCSC
3: 142281353 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
Q13535:p.Lys297Asn
NC_000003.11:g.142281353C>G
NC_000003.12:g.142562511C>G
... more HGVS
Protein change
K297N
Other names
-
Canonical SPDI
NC_000003.12:142562510:C:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.00300 (G)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00861
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.01184
1000 Genomes Project 0.00300
The Genome Aggregation Database (gnomAD) 0.01290
Links
ClinGen: CA171382
UniProtKB: Q13535#VAR_041586
dbSNP: rs2229033
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 3 criteria provided, multiple submitters, no conflicts Oct 11, 2017 RCV000145333.7
Benign 1 criteria provided, single submitter Oct 23, 2015 RCV000210817.1
Benign 1 criteria provided, single submitter Apr 27, 2017 RCV001147814.1
Benign 1 criteria provided, single submitter Jun 10, 2020 RCV001282494.1
Benign 2 criteria provided, single submitter Dec 8, 2020 RCV001512944.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ATR Little evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
704 723

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jul 02, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
(Autosomal recessive inheritance)
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000192412.1
Submitted: (Sep 11, 2014)
Comment:
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated … (more)
Evidence details
Benign
(Oct 23, 2015)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Vantari Genetics
Accession: SCV000266995.1
Submitted: (Mar 29, 2016)
Evidence details
Benign
(Oct 11, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000730060.1
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Seckel syndrome 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001308660.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (1)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Benign
(Jun 10, 2020)
criteria provided, single submitter
Method: clinical testing
none provided
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories
Accession: SCV001159512.2
Submitted: (Dec 11, 2020)
Evidence details
Benign
(Dec 08, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001720445.1
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Study: VKGL Data-share Consensus
Accession: SCV001799133.1
Submitted: (Aug 19, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001743946.3
Submitted: (Sep 02, 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
Mutation analysis of the ATR gene in breast and ovarian cancer families. Heikkinen K Breast cancer research : BCR 2005 PMID: 15987455

Text-mined citations for rs2229033...

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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 Sep 07, 2021