NM_000059.4(BRCA2):c.2960A>T (p.Asn987Ile) AND Breast-ovarian cancer, familial, susceptibility to, 2

Germline classification:: Benign (8 submissions)
Last evaluated:: Aug 10, 2015
Review status:: 3 stars out of maximum of 4 stars
reviewed by expert panel

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:: RCV000077289.24

Allele description [Variation Report for NM_000059.4(BRCA2):c.2960A>T (p.Asn987Ile)]

NM_000059.4(BRCA2):c.2960A>T (p.Asn987Ile)

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.2960A>T (p.Asn987Ile)

Other names:

N987I; p.N987I:AAT>ATT

HGVS:

NC_000013.11:g.32337315A>T
NG_012772.3:g.26836A>T
NM_000059.4:c.2960A>TMANE SELECT
NP_000050.2:p.Asn987Ile
NP_000050.3:p.Asn987Ile
LRG_293t1:c.2960A>T
LRG_293:g.26836A>T
LRG_293p1:p.Asn987Ile
NC_000013.10:g.32911452A>T
NM_000059.3:c.2960A>T
U43746.1:n.3188A>T
p.N987I

Nucleotide change:

3188A>T

Links:

dbSNP: rs2227944

NCBI 1000 Genomes Browser:

rs2227944

Molecular consequence:

NM_000059.4:c.2960A>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Breast-ovarian cancer, familial, susceptibility to, 2 (BROVCA2)
Synonyms:: Breast-ovarian cancer, familial 2
Identifiers:: MONDO: MONDO:0012933; MedGen: C2675520; Orphanet: 145; OMIM: 612555

Recent activity

Clear Turn Off Turn On

essv6958970 (3)
dbVar
GEO Profile Links for OMIM (Select 616226) (3678)
GEO Profiles
Homo sapiens neuregulin 2 (NRG2), transcript variant 8, mRNA
Homo sapiens neuregulin 2 (NRG2), transcript variant 8, mRNA
gi|2287254736|ref|NM_001410780.1|

Nucleotide

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000109086	Sharing Clinical Reports Project (SCRP)	no assertion criteria provided	Benign (May 1, 2012)	germline	clinical testing
SCV000146150	Breast Cancer Information Core (BIC) (BRCA2)	no assertion criteria provided	Benign (May 29, 2002)	germline	clinical testing
SCV000189895	Pathway Genomics	no assertion criteria provided	Likely benign (Jul 24, 2014)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 24728327, 21990134, 15744044, 11030418, 18284688, 18824701
SCV000195972	Michigan Medical Genetics Laboratories, University of Michigan	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Nov 3, 2014)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000220278	Counsyl	criteria provided, single submitter (Counsyl Autosomal Dominant Disease Classification criteria (2015))	Benign (Apr 29, 2014)	unknown	literature only	PubMed (6) [See all records that cite these PMIDs] 21990134, 11030418, 22811390, 18284688, 15744044, 18824701 Counsyl Autosomal Dominant Disease Classification criteria (2015), Citation Link,
SCV000244433	Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)	reviewed by expert panel (ENIGMA BRCA1/2 Classification Criteria (2015))	Benign (Aug 10, 2015)	germline	curation	PubMed (1) [See all records that cite this PMID] ENIGMA BRCA1/2 Classification Criteria (2015), Citation Link,
SCV000383666	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Feb 2, 2018)	germline	clinical testing	PubMed (9) [See all records that cite these PMIDs] 18284688, 21990134, 19795481, 22811390, 24489791, 15744044, 18824701, 24728327, 11030418 Citation Link,
SCV004016870	KCCC/NGS Laboratory, Kuwait Cancer Control Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Jul 7, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	11	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, curation
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	literature only
not provided	germline	not provided	2	not provided	not provided	2	not provided	clinical testing
African	germline	yes	21	not provided	not provided	not provided	not provided	clinical testing
African American	germline	yes	3	not provided	not provided	not provided	not provided	clinical testing
African, Latin American, Caribbean	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing
African, Native American	germline	yes	2	not provided	not provided	not provided	not provided	clinical testing
Trinidadian	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing
Western European, African, Native American	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing
Western European, Jamaican (Africian), Scottish	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Evaluation of unclassified variants in the breast cancer susceptibility genes BRCA1 and BRCA2 using five methods: results from a population-based study of young breast cancer patients.

Lee E, McKean-Cowdin R, Ma H, Chen Z, Van Den Berg D, Henderson BE, Bernstein L, Ursin G.

Breast Cancer Res. 2008;10(1):R19. doi: 10.1186/bcr1865. Epub 2008 Feb 19.

PubMed [citation]

PMID:: 18284688
PMCID:: PMC2374975

A review of a multifactorial probability-based model for classification of BRCA1 and BRCA2 variants of uncertain significance (VUS).

Lindor NM, Guidugli L, Wang X, Vallée MP, Monteiro AN, Tavtigian S, Goldgar DE, Couch FJ.

Hum Mutat. 2012 Jan;33(1):8-21. doi: 10.1002/humu.21627. Epub 2011 Nov 3. Review.

PubMed [citation]

PMID:: 21990134
PMCID:: PMC3242438

See all PubMed Citations (10)

Details of each submission

From Sharing Clinical Reports Project (SCRP), SCV000109086.5

#	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	not provided	2	not provided	not provided		not provided	not provided	not provided	See 1

Co-occurrences

#	Zygosity	Alleles	Number of Observations
1	SingleHeterozygote	BRCA2:3014T>C (L929S)	1

From Breast Cancer Information Core (BIC) (BRCA2), SCV000146150.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	9	not provided	not provided	clinical testing	not provided
2	not provided	1	not provided	not provided	clinical testing	not provided
3	not provided	1	not provided	not provided	clinical testing	not provided
4	African	21	not provided	not provided	clinical testing	not provided
5	African American	3	not provided	not provided	clinical testing	not provided
6	African, Latin American, Caribbean	1	not provided	not provided	clinical testing	not provided
7	African, Native American	2	not provided	not provided	clinical testing	not provided
8	Trinidadian	1	not provided	not provided	clinical testing	not provided
9	Western European, African, Native American	1	not provided	not provided	clinical testing	not provided
10	Western European, Jamaican (Africian), Scottish	1	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		9	not provided	not provided	not provided
2	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided
3	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided
4	germline	yes	not provided	not provided	not provided		21	not provided	not provided	not provided
5	germline	yes	not provided	not provided	not provided		3	not provided	not provided	not provided
6	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided
7	germline	yes	not provided	not provided	not provided		2	not provided	not provided	not provided
8	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided
9	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided
10	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

From Pathway Genomics, SCV000189895.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

#	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 Michigan Medical Genetics Laboratories, University of Michigan, SCV000195972.1

#	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	Blood	not provided		not provided	not provided	not provided	not provided

From Counsyl, SCV000220278.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (6)

#	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

From Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA), SCV000244433.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	PubMed (1)

Description

IARC class based on posterior probability from multifactorial likelihood analysis, thresholds for class as per Plon et al. 2008 (PMID: 18951446). Class 1 based on posterior probability = 0.0000741

#	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 Illumina Laboratory Services, Illumina, SCV000383666.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (9)

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

#	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 KCCC/NGS Laboratory, Kuwait Cancer Control Center, SCV004016870.1

#	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

Last Updated: Nov 10, 2024

Relating variation to medicine