NM_000059.4(BRCA2):c.4211del (p.Thr1403_Ser1404insTer) AND not provided

Germline classification:: Pathogenic (4 submissions)
Last evaluated:: Sep 24, 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:: RCV000478663.17

Allele description [Variation Report for NM_000059.4(BRCA2):c.4211del (p.Thr1403_Ser1404insTer)]

NM_000059.4(BRCA2):c.4211del (p.Thr1403_Ser1404insTer)

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.4211del (p.Thr1403_Ser1404insTer)

HGVS:

NC_000013.11:g.32338566del
NG_012772.3:g.28087del
NM_000059.4:c.4211delMANE SELECT
NP_000050.3:p.Thr1403_Ser1404insTer
LRG_293:g.28087del
NC_000013.10:g.32912703del
NC_000013.10:g.32912703delC
NM_000059.3:c.4211delC
NM_000059.4:c.4211del

Nucleotide change:

4439delC

Links:

dbSNP: rs398122777

NCBI 1000 Genomes Browser:

rs398122777

Molecular consequence:

NM_000059.4:c.4211del - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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thioredoxin H1-like [Benincasa hispida]
thioredoxin H1-like [Benincasa hispida]
gi|1955870364|ref|XP_038893093.1|

Protein
dai37a05.y1 NICHD_XGC_Sp1 Xenopus laevis cDNA clone IMAGE:4963856 5', mRNA seque...
dai37a05.y1 NICHD_XGC_Sp1 Xenopus laevis cDNA clone IMAGE:4963856 5', mRNA sequence
gi|15266890|gnl|dbEST|9284769|gb|BI 3.1|

Nucleotide
JGI_XZT9585.fwd NIH_XGC_tropTad5 Xenopus tropicalis cDNA clone IMAGE:7587384 5',...
JGI_XZT9585.fwd NIH_XGC_tropTad5 Xenopus tropicalis cDNA clone IMAGE:7587384 5', mRNA sequence
gi|57043842|gnl|dbEST|26935889|gb|C 25.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000567997	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Sep 24, 2024)	germline	clinical testing	Citation Link,
SCV001743376	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus	no assertion criteria provided	Pathogenic	germline	clinical testing
SCV001906018	Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Pathogenic	germline	clinical testing
SCV003810488	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Nov 29, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From GeneDx, SCV000567997.6

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

Description

Nonsense 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 4439delC; This variant is associated with the following publications: (PMID: 25151137, 29580149, 30787465, 36974724, 34428338, 29446198, 30039884, 20104584, 31892343, 31447099)

#	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 Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001743376.3

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

From Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute - VKGL Data-share Consensus, SCV001906018.1

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

From Revvity Omics, Revvity, SCV003810488.2

#	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

Last Updated: Nov 10, 2024

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