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NM_007294.3(BRCA1):c.4097-11T>C

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Interpretation:
Benign​

Review status:
reviewed by expert panel
Submissions:
9 (Most recent: Sep 13, 2021)
Last evaluated:
Aug 10, 2015
Accession:
VCV000125673.7
Variation ID:
125673
Description:
single nucleotide variant
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NM_007294.3(BRCA1):c.4097-11T>C

Allele ID
131211
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17q21.31
Genomic location
17: 43091043 (GRCh38) GRCh38 UCSC
17: 41243060 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_292:g.126941T>C
LRG_292t1:c.4097-11T>C
U14680.1:n.4216-11T>C
... more HGVS
Protein change
-
Other names
IVS11-11T>C
Canonical SPDI
NC_000017.11:43091042:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00000
Trans-Omics for Precision Medicine (TOPMed) 0.00002
Links
Breast Cancer Information Core (BIC) (BRCA1): 4216-11&base_change=T to C
BRCA1-HCI: BRCA1_00137
ClinGen: CA002622
dbSNP: rs80358072
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 4 reviewed by expert panel Aug 10, 2015 RCV000112253.2
Likely benign 1 criteria provided, single submitter Nov 25, 2020 RCV000123276.8
Likely benign 1 criteria provided, single submitter Nov 2, 2017 RCV000583619.1
Likely benign 1 criteria provided, single submitter Feb 27, 2019 RCV000855578.1
Benign 1 criteria provided, single submitter Mar 3, 2015 RCV001647081.1
Likely benign 1 no assertion criteria provided - RCV001357737.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
BRCA1 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
12270 12437

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Aug 10, 2015)
reviewed by expert panel
Method: curation
Breast-ovarian cancer, familial 1
Allele origin: germline
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)
Accession: SCV000244354.1
Submitted: (Aug 17, 2015)
Evidence details
Publications
PubMed (1)
Other databases
http://hci-exlovd.hci.utah.edu/v…
Comment:
IARC class based on posterior probability from multifactorial likelihood analysis, thresholds for class as per Plon et al. 2008 (PMID: 18951446). Class 1 based on … (more)
Likely benign
(Jul 14, 2017)
criteria provided, single submitter
Method: clinical testing
Breast-ovarian cancer, familial 1
Allele origin: unknown
Counsyl
Accession: SCV000785367.2
Submitted: (Jun 20, 2018)
Evidence details
Publications
PubMed (4)
Likely benign
(Feb 27, 2019)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000494378.2
Submitted: (Sep 24, 2019)
Evidence details
Publications
PubMed (8)
Comment:
Variant summary: BRCA1 c.4097-11T>C alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly … (more)
Likely benign
(Apr 21, 2016)
criteria provided, single submitter
Method: clinical testing
Breast-ovarian cancer, familial 1
Allele origin: germline
Michigan Medical Genetics Laboratories,University of Michigan
Accession: SCV000267709.1
Submitted: (Apr 21, 2016)
Evidence details
Likely benign
(Nov 02, 2017)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000688465.1
Submitted: (Dec 21, 2017)
Evidence details
Likely benign
(Nov 25, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary breast and ovarian cancer syndrome
Allele origin: germline
Invitae
Accession: SCV000166583.7
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Mar 03, 2015)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001857670.1
Submitted: (Sep 13, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 17924331, 21990134)
Uncertain significance
(Dec 23, 2003)
no assertion criteria provided
Method: clinical testing
Breast-ovarian cancer, familial 1
Allele origin: germline
Breast Cancer Information Core (BIC) (BRCA1)
Accession: SCV000144974.1
Submitted: (Mar 28, 2014)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
Malignant tumor of breast
Allele origin: unknown
Department of Pathology and Laboratory Medicine,Sinai Health System
Additional submitter:
Franklin by Genoox
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV001553297.1
Submitted: (Mar 31, 2021)
Evidence details
Comment:
The BRCA1 c.4097-11T>C variant was identified in 2 of 114056 proband chromosomes (frequency: 0.00002) from individuals or families with breast cancer (Borg 2010, Judkins 2005). … (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
Novel diagnostic tool for prediction of variant spliceogenicity derived from a set of 395 combined in silico/in vitro studies: an international collaborative effort. Leman R Nucleic acids research 2018 PMID: 29750258
Guidelines for splicing analysis in molecular diagnosis derived from a set of 327 combined in silico/in vitro studies on BRCA1 and BRCA2 variants. Houdayer C Human mutation 2012 PMID: 22505045
A review of a multifactorial probability-based model for classification of BRCA1 and BRCA2 variants of uncertain significance (VUS). Lindor NM Human mutation 2012 PMID: 21990134
Comprehensive prediction of mRNA splicing effects of BRCA1 and BRCA2 variants. Mucaki EJ Human mutation 2011 PMID: 21523855
Assessment of rare BRCA1 and BRCA2 variants of unknown significance using hierarchical modeling. Capanu M Genetic epidemiology 2011 PMID: 21520273
Characterization of BRCA1 and BRCA2 deleterious mutations and variants of unknown clinical significance in unilateral and bilateral breast cancer: the WECARE study. Borg A Human mutation 2010 PMID: 20104584
A systematic genetic assessment of 1,433 sequence variants of unknown clinical significance in the BRCA1 and BRCA2 breast cancer-predisposition genes. Easton DF American journal of human genetics 2007 PMID: 17924331
Application of embryonic lethal or other obvious phenotypes to characterize the clinical significance of genetic variants found in trans with known deleterious mutations. Judkins T Cancer research 2005 PMID: 16267036
http://hci-exlovd.hci.utah.edu/variants.php?select_db=BRCA1&action=search_all&search_Variant%2FDNA=c.4097-11T%3EC - - - -

Text-mined citations for rs80358072...

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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 18, 2021