NM_000059.4(BRCA2):c.7470_7478del (p.Ile2490_Asp2492del) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 6, 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:: RCV003293444.2

Allele description [Variation Report for NM_000059.4(BRCA2):c.7470_7478del (p.Ile2490_Asp2492del)]

NM_000059.4(BRCA2):c.7470_7478del (p.Ile2490_Asp2492del)

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.7470_7478del (p.Ile2490_Asp2492del)

HGVS:

NC_000013.11:g.32356462_32356470del
NG_012772.3:g.45983_45991del
NM_000059.4:c.7470_7478delMANE SELECT
NM_001406719.1:c.7374_7382del
NM_001406720.1:c.7470_7478del
NM_001406721.1:c.2538_2546del
NM_001406722.1:c.1053_1061del
NP_000050.2:p.Ile2490_Asp2492del
NP_000050.3:p.Ile2490_Asp2492del
NP_001393648.1:p.Ile2458_Asp2460del
NP_001393649.1:p.Ile2490_Asp2492del
NP_001393650.1:p.Ile846_Asp848del
NP_001393651.1:p.Ile351_Asp353del
LRG_293t1:c.7470_7478del
LRG_293:g.45983_45991del
LRG_293p1:p.Ile2490_Asp2492del
NC_000013.10:g.32930599_32930607del
NM_000059.3:c.7470_7478delACAGGATAT
NR_176251.1:n.7669_7677del

Molecular consequence:

NM_000059.4:c.7470_7478del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406719.1:c.7374_7382del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406720.1:c.7470_7478del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406721.1:c.2538_2546del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406722.1:c.1053_1061del - inframe_deletion - [Sequence Ontology: SO:0001822]
NR_176251.1:n.7669_7677del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004005532	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Jun 6, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004005532

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Jun 6, 2023)

germline

clinical testing

Citation Link

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

Details of each submission

From Ambry Genetics, SCV004005532.2

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

Description

The c.7470_7478delACAGGATAT variant (also known as p.I2490_D2492del) is located in coding exon 14 of the BRCA2 gene. This variant results from an in-frame ACAGGATAT deletion at nucleotide positions 7470 to 7478. This results in the in-frame deletion of an isoleucine, glutamine, and aspartic acid at codons 2490 to 2492. This amino acid region is generally not well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis (Choi Y et al. PLoS ONE. 2012; 7(10):e46688). Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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 1, 2024

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