NM_000059.4(BRCA2):c.3860del (p.Asn1287fs) AND not provided

Germline classification:: Pathogenic (6 submissions)
Last evaluated:: Aug 5, 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:: RCV000212232.39

Allele description [Variation Report for NM_000059.4(BRCA2):c.3860del (p.Asn1287fs)]

NM_000059.4(BRCA2):c.3860del (p.Asn1287fs)

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.3860del (p.Asn1287fs)

Other names:

4088delA; 4082delA

HGVS:

NC_000013.11:g.32338215del
NG_012772.3:g.27736del
NM_000059.4:c.3860delMANE SELECT
NP_000050.3:p.Asn1287fs
LRG_293:g.27736del
NC_000013.10:g.32912346del
NC_000013.10:g.32912352del
NC_000013.10:g.32912352delA
NC_000013.11:g.32338215delA
NM_000059.3:c.3854_3854delA
NM_000059.3:c.3854delA
NM_000059.3:c.3860delA
NM_000059.4:c.3860del
U43746.1:n.4082delA
U43746.1:n.4088delA
p.Asn1287Ilefs*6
p.N1287IfsX6

Nucleotide change:

4088DELA

Links:

Breast Cancer Information Core (BIC) (BRCA2): 4082&base_change=del A; Breast Cancer Information Core (BIC) (BRCA2): 4088&base_change=del A; dbSNP: rs80359406

NCBI 1000 Genomes Browser:

rs80359406

Molecular consequence:

NM_000059.4:c.3860del - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

Condition(s)

Synonyms:: none provided; RECLASSIFIED - ADRA2C POLYMORPHISM; RECLASSIFIED - ADRB1 POLYMORPHISM
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000210740	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Apr 3, 2024)	germline	clinical testing	Citation Link,
SCV000600567	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Pathogenic (May 24, 2017)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 11857748, 24156927, 23199084, 12942367, 26467025
SCV001447001	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Oct 23, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001501470	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Jun 1, 2021)	germline	clinical testing	Citation Link,
SCV005199784	Clinical Genetics Laboratory, Skane University Hospital Lund	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (May 27, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005414147	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Aug 5, 2024)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 28724667, 31528241, 31742824, 25741868

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	2	not provided	not provided	1	not provided	clinical testing
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Low frequency of recurrent BRCA1 and BRCA2 mutations in Spain.

Llort G, Muñoz CY, Tuser MP, Guillermo IB, Lluch JR, Bale AE, Franco MA.

Hum Mutat. 2002 Mar;19(3):307.

PubMed [citation]

PMID:: 11857748

Central European BRCA2 mutation carriers: birth cohort status correlates with onset of breast cancer.

Tea MK, Kroiss R, Muhr D, Fuerhauser-Rappaport C, Oefner P, Wagner TM, Singer CF.

Maturitas. 2014 Jan;77(1):68-72. doi: 10.1016/j.maturitas.2013.09.012. Epub 2013 Oct 1.

PubMed [citation]

PMID:: 24156927

See all PubMed Citations (9)

Details of each submission

From GeneDx, SCV000210740.13

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

Description

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; Also known as 4088del; This variant is associated with the following publications: (PMID: 18821011, 27167707, 34413315, 32438681, 29884136, 11857748, 23199084, 24156927, 12673801, 26843898, 26681312, 26848529, 27393621, 28480178, 29339979, 28724667, 30702160, 31528241, 31825140, 30787465, 31742824, 33087929, 32885271, 35803546, 34645131, 35864222, 36495689, 33471991)

#	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, SCV000600567.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

#	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 Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, SCV001447001.1

#	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	yes	1	not provided	not provided		not provided	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV001501470.23

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	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	germline	yes	not provided	not provided	not provided		2	not provided	not provided	not provided

From Clinical Genetics Laboratory, Skane University Hospital Lund, SCV005199784.1

#	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	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Mayo Clinic Laboratories, Mayo Clinic, SCV005414147.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (4)

Description

PM5_strong, PVS1

#	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		1	not provided	not provided	not provided

Last Updated: Nov 30, 2024

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