NM_000059.4(BRCA2):c.8872_8880del (p.Lys2958_Gln2960del) AND Hereditary breast ovarian cancer syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 27, 2023
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:: RCV003644645.2

Allele description [Variation Report for NM_000059.4(BRCA2):c.8872_8880del (p.Lys2958_Gln2960del)]

NM_000059.4(BRCA2):c.8872_8880del (p.Lys2958_Gln2960del)

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.8872_8880del (p.Lys2958_Gln2960del)

HGVS:

NC_000013.11:g.32379434_32379442del
NG_012772.3:g.68955_68963del
NM_000059.4:c.8872_8880delMANE SELECT
NM_001406719.1:c.8776_8784del
NM_001406720.1:c.8872_8880del
NM_001406721.1:c.3940_3948del
NM_001406722.1:c.2455_2463del
NP_000050.2:p.Lys2958_Gln2960del
NP_000050.3:p.Lys2958_Gln2960del
NP_001393648.1:p.Lys2926_Gln2928del
NP_001393649.1:p.Lys2958_Gln2960del
NP_001393650.1:p.Lys1314_Gln1316del
NP_001393651.1:p.Lys819_Gln821del
LRG_293t1:c.8872_8880del
LRG_293:g.68955_68963del
LRG_293p1:p.Lys2958_Gln2960del
NC_000013.10:g.32953565_32953573del
NC_000013.10:g.32953571_32953579del
NM_000059.3:c.8872_8880delAAGGAACAA
NR_176251.1:n.9135_9143del

Molecular consequence:

NM_000059.4:c.8872_8880del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406719.1:c.8776_8784del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406720.1:c.8872_8880del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406721.1:c.3940_3948del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406722.1:c.2455_2463del - inframe_deletion - [Sequence Ontology: SO:0001822]
NR_176251.1:n.9135_9143del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV004458613	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Apr 27, 2023)	germline	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

SCV004458613

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Apr 27, 2023)

germline

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	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

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004458613.1

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with BRCA2-related conditions. This variant is not present in population databases (gnomAD no frequency). This variant, c.8872_8880del, results in the deletion of 3 amino acid(s) of the BRCA2 protein (p.Lys2958_Gln2960del), but otherwise preserves the integrity of the reading frame.

#	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

Last Updated: Sep 29, 2024

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