NM_000059.4(BRCA2):c.3865_3868del (p.Lys1289fs) AND Familial cancer of breast

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Feb 20, 2024
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV002250487.11

Allele description [Variation Report for NM_000059.4(BRCA2):c.3865_3868del (p.Lys1289fs)]

NM_000059.4(BRCA2):c.3865_3868del (p.Lys1289fs)

Gene:

BRCA2:BRCA2 DNA repair associated [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

13q13.1

Genomic location:

Preferred name:

NM_000059.4(BRCA2):c.3865_3868del (p.Lys1289fs)

Other names:

NP_000050.3:p.Lys1289AlafsTer3

HGVS:

NC_000013.10:g.32912354_32912357del
NC_000013.11:g.32338220_32338223del
NG_012772.3:g.27741_27744del
NM_000059.4:c.3865_3868delMANE SELECT
NP_000050.3:p.Lys1289fs
LRG_293:g.27741_27744del
NC_000013.10:g.32912354_32912357del
NC_000013.10:g.32912357_32912360del
NC_000013.10:g.32912357_32912360delAAAT
NM_000059.3:c.3862_3865del
NM_000059.3:c.3865_3868delAAAT
NM_000059.4:c.3865_3868del
U43746.1:n.4093_4096del4
U43746.1:n.4093_4096delAAAT
p.Lys1289Alafs*3

Nucleotide change:

4093del4

Links:

Breast Cancer Information Core (BIC) (BRCA2): 4093&base_change=del 4; dbSNP: rs80359412

NCBI 1000 Genomes Browser:

rs80359412

Molecular consequence:

NM_000059.4:c.3865_3868del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Familial cancer of breast
Synonyms:: Breast cancer, familial; Hereditary breast cancer
Identifiers:: MONDO: MONDO:0016419; MedGen: C0346153; OMIM: 114480

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002520786	Center for Precision Medicine, Meizhou People's Hospital	no assertion criteria provided	Pathogenic	germline	literature only	PubMed (3) [See all records that cite these PMIDs] 28492532, 22729890, 20104584
SCV004211925	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Feb 20, 2024)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002520786

Center for Precision Medicine, Meizhou People's Hospital

no assertion criteria provided

Pathogenic

germline

literature only

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

SCV004211925

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Feb 20, 2024)

unknown

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	literature only
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

A 24-color metaphase-based radiation assay discriminates heterozygous BRCA2 mutation carriers from controls by chromosomal radiosensitivity.

Becker AA, Graeser MK, Landwehr C, Hilger T, Baus W, Wappenschmidt B, Meindl A, Weber RG, Schmutzler RK.

Breast Cancer Res Treat. 2012 Aug;135(1):167-75. doi: 10.1007/s10549-012-2119-0. Epub 2012 Jun 23.

PubMed [citation]

PMID:: 22729890

See all PubMed Citations (4)

Details of each submission

From Center for Precision Medicine, Meizhou People's Hospital, SCV002520786.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (3)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Baylor Genetics, SCV004211925.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 20, 2024

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