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NM_007294.4(BRCA1):c.3305A>G (p.Asn1102Ser)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(2);Uncertain significance(4)

Review status:
criteria provided, conflicting interpretations
Submissions:
8 (Most recent: Sep 9, 2021)
Last evaluated:
Oct 5, 2020
Accession:
VCV000054831.7
Variation ID:
54831
Description:
single nucleotide variant
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NM_007294.4(BRCA1):c.3305A>G (p.Asn1102Ser)

Allele ID
69498
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17q21.31
Genomic location
17: 43092226 (GRCh38) GRCh38 UCSC
17: 41244243 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_007294.3:c.3305A>G NP_009225.1:p.Asn1102Ser missense
NC_000017.10:g.41244243T>C
NC_000017.11:g.43092226T>C
... more HGVS
Protein change
N1102S, N1055S
Other names
-
Canonical SPDI
NC_000017.11:43092225:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00001
Exome Aggregation Consortium (ExAC) 0.00002
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Links
ClinGen: CA002133
dbSNP: rs80356900
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Feb 24, 2020 RCV000506903.2
Uncertain significance 1 criteria provided, single submitter Oct 5, 2020 RCV001350762.1
Likely benign 1 criteria provided, single submitter Jan 20, 2020 RCV001662058.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Sep 28, 2019 RCV000214206.2
Uncertain significance 1 no assertion criteria provided Feb 20, 2004 RCV000112054.1
Uncertain significance 1 no assertion criteria provided Jun 1, 2020 RCV001582548.1
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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
Uncertain significance
(Feb 24, 2020)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001338189.1
Submitted: (Apr 29, 2020)
Evidence details
Publications
PubMed (5)
Comment:
Variant summary: BRCA1 c.3305A>G (p.Asn1102Ser) results in a conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a benign … (more)
Likely benign
(May 08, 2017)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV001344321.1
Submitted: (May 19, 2020)
Evidence details
Uncertain significance
(Sep 28, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000274806.5
Submitted: (Nov 30, 2020)
Evidence details
Publications
PubMed (1)
Comment:
The p.N1102S variant (also known as c.3305A>G), located in coding exon 9 of the BRCA1 gene, results from an A to G substitution at nucleotide … (more)
Uncertain significance
(Oct 05, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary breast and ovarian cancer syndrome
Allele origin: germline
Invitae
Accession: SCV001545180.1
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (2)
Comment:
This sequence change replaces asparagine with serine at codon 1102 of the BRCA1 protein (p.Asn1102Ser). The asparagine residue is moderately conserved and there is a … (more)
Uncertain significance
(Jun 07, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV000600325.1
Submitted: (Aug 01, 2017)
Evidence details
Publications
PubMed (4)
Likely benign
(Jan 20, 2020)
criteria provided, single submitter
Method: curation
Breast-ovarian cancer, familial 1
Breast-ovarian cancer, familial 2
Hereditary breast and ovarian cancer syndrome
Allele origin: germline
Research and Development, ARUP Laboratories
Accession: SCV001878300.1
Submitted: (Sep 09, 2021)
Evidence details
Publications
PubMed (1)
Other databases
https://arup.utah.edu/database/B…
Uncertain significance
(Feb 20, 2004)
no assertion criteria provided
Method: clinical testing
Breast-ovarian cancer, familial 1
Allele origin: germline
Breast Cancer Information Core (BIC) (BRCA1)
Accession: SCV000144707.1
Submitted: (Mar 28, 2014)
Evidence details
Uncertain significance
(Jun 01, 2020)
no assertion criteria provided
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001811353.1
Submitted: (Aug 31, 2021)
Evidence details
Comment:
Not observed at a significant frequency in large population cohorts (Lek 2016); In silico analysis supports that this missense variant has a deleterious effect on … (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
Large scale multifactorial likelihood quantitative analysis of BRCA1 and BRCA2 variants: An ENIGMA resource to support clinical variant classification. Parsons MT Human mutation 2019 PMID: 31131967
BRCA1- and BRCA2-specific in silico tools for variant interpretation in the CAGI 5 ENIGMA challenge. Padilla N Human mutation 2019 PMID: 31112341
Benchmarking mutation effect prediction algorithms using functionally validated cancer-related missense mutations. Martelotto LG Genome biology 2014 PMID: 25348012
Three novel BRCA1/BRCA2 mutations in breast/ovarian cancer families in Croatia. Levanat S Gene 2012 PMID: 22366370
EMMA, a cost- and time-effective diagnostic method for simultaneous detection of point mutations and large-scale genomic rearrangements: application to BRCA1 and BRCA2 in 1,525 patients. Caux-Moncoutier V Human mutation 2011 PMID: 21120943
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
Evolution of the tumor suppressor BRCA1 locus in primates: implications for cancer predisposition. Pavlicek A Human molecular genetics 2004 PMID: 15385441
https://arup.utah.edu/database/BRCA/Variants/BRCA1.php - - - -

Text-mined citations for rs80356900...

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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