rs80359254

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6

The NM_000059.4(BRCA2):ā€‹c.9934A>Gā€‹(p.Ile3312Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,614,244 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: š‘“ 0.0000066 ( 0 hom., cov: 32)
Exomes š‘“: 0.000014 ( 0 hom. )

Consequence

BRCA2
NM_000059.4 missense

Scores

16

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:9B:2

Conservation

PhyloP100: -0.791
Variant links:
Genes affected
BRCA2 (HGNC:1101): (BRCA2 DNA repair associated) Inherited mutations in BRCA1 and this gene, BRCA2, confer increased lifetime risk of developing breast or ovarian cancer. Both BRCA1 and BRCA2 are involved in maintenance of genome stability, specifically the homologous recombination pathway for double-strand DNA repair. The largest exon in both genes is exon 11, which harbors the most important and frequent mutations in breast cancer patients. The BRCA2 gene was found on chromosome 13q12.3 in human. The BRCA2 protein contains several copies of a 70 aa motif called the BRC motif, and these motifs mediate binding to the RAD51 recombinase which functions in DNA repair. BRCA2 is considered a tumor suppressor gene, as tumors with BRCA2 mutations generally exhibit loss of heterozygosity (LOH) of the wild-type allele. [provided by RefSeq, May 2020]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.030410051).
BP6
Variant 13-32398447-A-G is Benign according to our data. Variant chr13-32398447-A-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 38265.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=2, Uncertain_significance=6}. Variant chr13-32398447-A-G is described in Lovd as [Likely_benign].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
BRCA2NM_000059.4 linkuse as main transcriptc.9934A>G p.Ile3312Val missense_variant 27/27 ENST00000380152.8 NP_000050.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
BRCA2ENST00000380152.8 linkuse as main transcriptc.9934A>G p.Ile3312Val missense_variant 27/275 NM_000059.4 ENSP00000369497 A2

Frequencies

GnomAD3 genomes
AF:
0.00000657
AC:
1
AN:
152254
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000159
AC:
4
AN:
251266
Hom.:
0
AF XY:
0.0000221
AC XY:
3
AN XY:
135806
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000264
Gnomad OTH exome
AF:
0.000163
GnomAD4 exome
AF:
0.0000144
AC:
21
AN:
1461872
Hom.:
0
Cov.:
31
AF XY:
0.0000179
AC XY:
13
AN XY:
727234
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000232
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000153
Gnomad4 OTH exome
AF:
0.0000331
GnomAD4 genome
AF:
0.00000656
AC:
1
AN:
152372
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
74506
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.00000756
ExAC
AF:
0.00000824
AC:
1
Asia WGS
AF:
0.000577
AC:
2
AN:
3478
EpiCase
AF:
0.0000545
EpiControl
AF:
0.00

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:9Benign:2
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 2 Uncertain:4Benign:1
Uncertain significance, no assertion criteria providedclinical testingSharing Clinical Reports Project (SCRP)Jan 24, 2007- -
Uncertain significance, criteria provided, single submitterclinical testingKCCC/NGS Laboratory, Kuwait Cancer Control CenterJun 06, 2023This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 3312 of the BRCA2 protein (p.Ile3312Val). This variant is present in population databases (rs80359254, gnomAD 0.003%). This missense change has been observed in individual(s) with a personal or family history of breast or ovarian cancer (PMID: 18779604, 27124784, 31273614). ClinVar contains an entry for this variant (Variation ID: 38265). . In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance -
Uncertain significance, no assertion criteria providedclinical testingBreast Cancer Information Core (BIC) (BRCA2)Dec 23, 2003- -
Likely benign, criteria provided, single submitterclinical testingAll of Us Research Program, National Institutes of HealthNov 20, 2023- -
Uncertain significance, criteria provided, single submitterclinical testingCounsylJan 27, 2016- -
Hereditary cancer-predisposing syndrome Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsJun 20, 2023The p.I3312V variant (also known as c.9934A>G), located in coding exon 26 of the BRCA2 gene, results from an A to G substitution at nucleotide position 9934. The isoleucine at codon 3312 is replaced by valine, an amino acid with highly similar properties. This alteration has been identified in individuals diagnosed with breast and/or ovarian cancer (Gervas P et al. Mol Biol Rep, 2019 Oct;46:5537-5541; Tariq H et al. Asian Pac J Cancer Prev, 2021 Mar;22:719-724). Additionally, this variant was reported in 2/60,466 breast cancer cases and in 1/53,461 controls (Dorling et al. N Engl J Med. 2021 02;384:428-439).This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
Likely benign, criteria provided, single submitterclinical testingColor Diagnostics, LLC DBA Color HealthOct 17, 2016- -
not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingWomen's Health and Genetics/Laboratory Corporation of America, LabCorpJul 01, 2024Variant summary: BRCA2 c.9934A>G (p.Ile3312Val) results in a conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 1.6e-05 in 251266 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.9934A>G has been reported in the literature in individuals affected with breast cancer (e.g. Park_2016, Gervas_2019, Tariq_2021, Onsekiz_2021, Senturk_2021, Yao_2022) and premature ovarian insufficiency (e.g. Yilmaz_2016), without strong evidence for causality. These reports do not provide unequivocal conclusions about association of the variant with Hereditary Breast And Ovarian Cancer Syndrome. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 31273614, 34658299, 27124784, 34828379, 28422718, 33773534, 35864222, 27403073). ClinVar contains an entry for this variant (Variation ID: 38265). Based on the evidence outlined above, the variant was classified as uncertain significance. -
BRCA2-related disorder Uncertain:1
Uncertain significance, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesAug 26, 2024The BRCA2 c.9934A>G variant is predicted to result in the amino acid substitution p.Ile3312Val. This variant has been reported as a variant of uncertain significance in several individuals with a personal history of breast and/or ovarian cancer (Tariq H et al 2021. PubMed ID: 33773534; Gervas P et al 2019. PubMed ID: 31273614; Senturk et al. 2021. PubMed ID: 34828379; Supp. Table 2 Yao et al 2022. PubMed ID: 35864222). This variant is reported in 0.0026% of alleles in individuals of European (non-Finnish) descent in gnomAD and has conflicting interpretations of likely benign and uncertain in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/38265/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
not provided Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingGeneDxJun 24, 2024Observed in individuals with personal and/or family history of breast and/or ovarian cancer (PMID: 18779604, 27124784, 31273614, 33471991, 34658299, 34828379, 33773534, 35864222); In silico analysis indicates that this missense variant does not alter protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); Also known as 10162A>G; This variant is associated with the following publications: (PMID: 27403073, 20435227, 16011303, 18779604, 16683254, 27124784, 31273614, 34658299, 10733923, 33471991, 34828379, 28422718, 35864222, 33773534) -
Hereditary breast ovarian cancer syndrome Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpFeb 01, 2024This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 3312 of the BRCA2 protein (p.Ile3312Val). This variant is present in population databases (rs80359254, gnomAD 0.003%). This missense change has been observed in individual(s) with a personal or family history of breast or ovarian cancer (PMID: 18779604, 27124784, 31273614, 33773534, 34828379). ClinVar contains an entry for this variant (Variation ID: 38265). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt BRCA2 protein function with a negative predictive value of 95%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.062
BayesDel_addAF
Benign
-0.38
T
BayesDel_noAF
Benign
-0.72
CADD
Benign
6.4
DANN
Benign
0.50
Eigen
Benign
-1.6
Eigen_PC
Benign
-1.6
FATHMM_MKL
Benign
0.027
N
M_CAP
Benign
0.035
D
MetaRNN
Benign
0.030
T;T
MetaSVM
Benign
-0.89
T
MutationTaster
Benign
1.0
N;N
PrimateAI
Benign
0.24
T
PROVEAN
Benign
-0.070
N;N
REVEL
Benign
0.017
Sift
Benign
0.57
T;T
Sift4G
Benign
0.98
T;T
Vest4
0.044
MutPred
0.10
Loss of catalytic residue at L3317 (P = 0.0706);Loss of catalytic residue at L3317 (P = 0.0706);
MVP
0.65
MPC
0.020
ClinPred
0.032
T
GERP RS
-8.0
gMVP
0.087

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs80359254; hg19: chr13-32972584; API