NM_000059.4(BRCA2):c.4258G>T (p.Asp1420Tyr) AND Hereditary breast ovarian cancer syndrome

Germline classification:: Benign (5 submissions)
Last evaluated:: Feb 1, 2024
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:: RCV000044377.31

Allele description [Variation Report for NM_000059.4(BRCA2):c.4258G>T (p.Asp1420Tyr)]

NM_000059.4(BRCA2):c.4258G>T (p.Asp1420Tyr)

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.4258G>T (p.Asp1420Tyr)

Other names:

p.D1420Y:GAT>TAT; NP_000050.3:p.Asp1420Tyr

HGVS:

NC_000013.11:g.32338613G>T
NG_012772.3:g.28134G>T
NM_000059.4:c.4258G>TMANE SELECT
NP_000050.2:p.Asp1420Tyr
NP_000050.3:p.Asp1420Tyr
LRG_293t1:c.4258G>T
LRG_293:g.28134G>T
LRG_293p1:p.Asp1420Tyr
NC_000013.10:g.32912750G>T
NM_000059.3:c.4258G>T
NM_000059.4:c.4258G>T
U43746.1:n.4486G>T
p.D1420Y

Nucleotide change:

4486G>T

Protein change:

D1420Y

Links:

dbSNP: rs28897727

NCBI 1000 Genomes Browser:

rs28897727

Molecular consequence:

NM_000059.4:c.4258G>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Hereditary breast ovarian cancer syndrome
Synonyms:: Hereditary breast and ovarian cancer syndrome; Hereditary breast and ovarian cancer; Hereditary breast and ovarian cancer syndrome (HBOC); See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0003582; MeSH: D061325; MedGen: C0677776; Orphanet: 145

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000072390	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Feb 1, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000296855	Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia	criteria provided, single submitter (DGD Variant Analysis Guidelines)	Benign (Aug 24, 2015)	unknown	clinical testing	DGD_Variant_Analysis_Guidelines.docx, Citation Link,
SCV000494324	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (Apr 7, 2014)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 16905680, 12215251, 18284688, 15635067, 14507240, 23767878 LabCorp Variant Classification Summary - May 2015.docx, Citation Link,
SCV002026101	National Health Laboratory Service, Universitas Academic Hospital and University of the Free State	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Nov 16, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002515273	Genetics Program, Instituto Nacional de Cancer	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Nov 1, 2021)	germline	research	PubMed (2) [See all records that cite these PMIDs] 25741868, 36329109

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing, research
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
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

Evaluation of BRCA1 and BRCA2 mutation prevalence, risk prediction models and a multistep testing approach in French-Canadian families with high risk of breast and ovarian cancer.

Simard J, Dumont M, Moisan AM, Gaborieau V, Malouin H, Durocher F, Chiquette J, Plante M, Avard D, Bessette P, Brousseau C, Dorval M, Godard B, Houde L; INHERIT BRCAs, Joly Y, Lajoie MA, Leblanc G, Lépine J, Lespérance B, Vézina H, Parboosingh J, et al.

J Med Genet. 2007 Feb;44(2):107-21. Epub 2006 Aug 11. Erratum in: J Med Genet. 2007 Jul;44(7):471.

PubMed [citation]

PMID:: 16905680
PMCID:: PMC2598057

See all PubMed Citations (9)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000072390.14

#	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	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, SCV000296855.3

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

#	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

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000494324.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

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

From National Health Laboratory Service, Universitas Academic Hospital and University of the Free State, SCV002026101.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	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	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

From Genetics Program, Instituto Nacional de Cancer, SCV002515273.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	research	PubMed (2)

#	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

Last Updated: Dec 22, 2024

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