NM_000059.4(BRCA2):c.2956AAT[1] (p.Asn987del) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Sep 21, 2020
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:: RCV000160275.2

Allele description [Variation Report for NM_000059.4(BRCA2):c.2956AAT[1] (p.Asn987del)]

NM_000059.4(BRCA2):c.2956AAT[1] (p.Asn987del)

Gene:

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

Variant type:

Microsatellite

Cytogenetic location:

13q13.1

Genomic location:

Preferred name:

NM_000059.4(BRCA2):c.2956AAT[1] (p.Asn987del)

HGVS:

NC_000013.11:g.32337311AAT[1]
NG_012772.3:g.26832AAT[1]
NM_000059.4:c.2956AAT[1]MANE SELECT
NP_000050.3:p.Asn987del
LRG_293t1:c.2959_2961del
LRG_293:g.26832AAT[1]
NC_000013.10:g.32911448AAT[1]
NC_000013.10:g.32911448_32911450del
NM_000059.3:c.2959_2961del
NM_000059.3:c.2959_2961delAAT
p.N987del

Protein change:

N987del

Links:

dbSNP: rs730881603

NCBI 1000 Genomes Browser:

rs730881603

Molecular consequence:

NM_000059.4:c.2956AAT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Clinopodium betulifolium internal transcribed spacer 1, partial sequence; 5.8S r...
Clinopodium betulifolium internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence
gi|307556921|gb|GU012001.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000210728	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Uncertain significance (Mar 7, 2018)	germline	clinical testing	Citation Link,
SCV002046234	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Uncertain significance (Sep 21, 2020)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 30185652, 26467025

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000210728

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Uncertain significance
(Mar 7, 2018)

germline

clinical testing

Citation Link,

SCV002046234

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Uncertain significance
(Sep 21, 2020)

unknown

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A machine learning approach for somatic mutation discovery.

Wood DE, White JR, Georgiadis A, Van Emburgh B, Parpart-Li S, Mitchell J, Anagnostou V, Niknafs N, Karchin R, Papp E, McCord C, LoVerso P, Riley D, Diaz LA Jr, Jones S, Sausen M, Velculescu VE, Angiuoli SV.

Sci Transl Med. 2018 Sep 5;10(457). doi:pii: eaar7939. 10.1126/scitranslmed.aar7939.

PubMed [citation]

PMID:: 30185652
PMCID:: PMC6481619

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

Details of each submission

From GeneDx, SCV000210728.5

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

Description

This in-frame deletion of three nucleotides in BRCA2 is denoted c.2959_2961delAAT at the cDNA level and p.Asn987del (N987del) at the protein level. The normal sequence, with the bases that are deleted in brackets, is AAAT[delAAT]GATT. This variant has not, to our knowledge, been published in the literature as pathogenic or benign. This variant was not observed in large population cohorts (Lek 2016). This deletion of a single Asparagine amino acid is not located in a known functional domain. In-silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect. Since in-frame deletions may or may not inhibit proper protein functioning, the clinical significance of this finding remains unclear at this time. We consider BRCA2 Asn987del to be a variant of uncertain significance.

#	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 Quest Diagnostics Nichols Institute San Juan Capistrano, SCV002046234.1

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

#	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: Sep 29, 2024

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