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NM_000059.4(BRCA2):c.3262C>T (p.Pro1088Ser) AND Hereditary cancer-predisposing syndrome

Germline classification:
Benign/Likely benign (4 submissions)
Last evaluated:
Mar 23, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000129258.19

Allele description [Variation Report for NM_000059.4(BRCA2):c.3262C>T (p.Pro1088Ser)]

NM_000059.4(BRCA2):c.3262C>T (p.Pro1088Ser)

Gene:
BRCA2:BRCA2 DNA repair associated [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
13q13.1
Genomic location:
Preferred name:
NM_000059.4(BRCA2):c.3262C>T (p.Pro1088Ser)
Other names:
p.P1088S:CCT>TCT
HGVS:
  • NC_000013.11:g.32337617C>T
  • NG_012772.3:g.27138C>T
  • NM_000059.4:c.3262C>TMANE SELECT
  • NP_000050.2:p.Pro1088Ser
  • NP_000050.3:p.Pro1088Ser
  • LRG_293t1:c.3262C>T
  • LRG_293:g.27138C>T
  • LRG_293p1:p.Pro1088Ser
  • NC_000013.10:g.32911754C>T
  • NM_000059.3:c.3262C>T
  • U43746.1:n.3490C>T
  • p.P1088S
Nucleotide change:
3490C>T
Protein change:
P1088S
Links:
dbSNP: rs80358572
NCBI 1000 Genomes Browser:
rs80358572
Molecular consequence:
  • NM_000059.4:c.3262C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000184018Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)
Likely benign
(Oct 31, 2018)
germlineclinical testing

Citation Link,

SCV000902754Color Diagnostics, LLC DBA Color Health
criteria provided, single submitter

(ACMG Guidelines, 2015)
Benign
(Jun 22, 2016)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002533777Sema4, Sema4
criteria provided, single submitter

(Sema4 Curation Guidelines)
Likely benign
(Jan 10, 2022)
germlinecuration

PubMed (3)
[See all records that cite these PMIDs]

Citation Link,

SCV003851815University of Washington Department of Laboratory Medicine, University of Washington
criteria provided, single submitter

(Dines et al. (Genet Med. 2020))
Likely benign
(Mar 23, 2023)
germlinecuration

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing, curation

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Germ-line variants identified by next generation sequencing in a panel of estrogen and cancer associated genes correlate with poor clinical outcome in Lynch syndrome patients.

Jóri B, Kamps R, Xanthoulea S, Delvoux B, Blok MJ, Van de Vijver KK, de Koning B, Oei FT, Tops CM, Speel EJ, Kruitwagen RF, Gomez-Garcia EB, Romano A.

Oncotarget. 2015 Dec 1;6(38):41108-22. doi: 10.18632/oncotarget.5694.

PubMed [citation]
PMID:
26517685
PMCID:
PMC4747393
See all PubMed Citations (5)

Details of each submission

From Ambry Genetics, SCV000184018.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Color Diagnostics, LLC DBA Color Health, SCV000902754.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Sema4, Sema4, SCV002533777.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (3)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From University of Washington Department of Laboratory Medicine, University of Washington, SCV003851815.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (1)

Description

Missense variant in a coldspot region where missense variants are very unlikely to be pathogenic (PMID:31911673).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 30, 2024