NM_000059.4(BRCA2):c.3073A>G (p.Lys1025Glu) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (4 submissions)
Last evaluated:: Feb 11, 2022
Review status:: criteria provided, conflicting classifications

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:: RCV000586348.23

Allele description [Variation Report for NM_000059.4(BRCA2):c.3073A>G (p.Lys1025Glu)]

NM_000059.4(BRCA2):c.3073A>G (p.Lys1025Glu)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

13q13.1

Genomic location:

Preferred name:

NM_000059.4(BRCA2):c.3073A>G (p.Lys1025Glu)

Other names:

p.K1025E:AAG>GAG

HGVS:

NC_000013.11:g.32337428A>G
NG_012772.3:g.26949A>G
NM_000059.4:c.3073A>GMANE SELECT
NP_000050.2:p.Lys1025Glu
NP_000050.3:p.Lys1025Glu
LRG_293t1:c.3073A>G
LRG_293:g.26949A>G
LRG_293p1:p.Lys1025Glu
NC_000013.10:g.32911565A>G
NM_000059.3:c.3073A>G
U43746.1:n.3301A>G
p.K1025E

Nucleotide change:

3301A>G

Protein change:

K1025E

Links:

dbSNP: rs80358550

NCBI 1000 Genomes Browser:

rs80358550

Molecular consequence:

NM_000059.4:c.3073A>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000210586	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Dec 19, 2019)	germline	clinical testing	Citation Link,
SCV000805684	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jan 10, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001716148	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Nov 14, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004219566	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Likely benign (Feb 11, 2022)	unknown	clinical testing	PubMed (13) [See all records that cite these PMIDs] 32599251, 34178674, 25111659, 17679929, 33471991, 26941049, 25348012, 32123317, 30995915, 31131967, 22476429, 24504028, 26467025

Help

Summary from all submissions

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

Characterization and in silico analyses of the BRCA1/2 variants identified in individuals with personal and/or family history of BRCA-related cancers.

Pirim D, Kaya N, Yıldırım EU, Sag SO, Temel SG.

Int J Biol Macromol. 2020 Nov 1;162:1166-1177. doi: 10.1016/j.ijbiomac.2020.06.222. Epub 2020 Jun 26.

PubMed [citation]

PMID:: 32599251

See all PubMed Citations (14)

Details of each submission

From GeneDx, SCV000210586.14

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

Description

This variant is associated with the following publications: (PMID: 32123317, 31131967, 30995915, 28726806, 25348012, 26941049, 22476429, 17679929, 24504028, 25111659)

#	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 PreventionGenetics, part of Exact Sciences, SCV000805684.1

#	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	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Mayo Clinic Laboratories, Mayo Clinic, SCV001716148.1

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

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV004219566.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (13)

#	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: Nov 24, 2024

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