chr13-32379878-G-C

Position:

• chr13-32379878-G-C

Variant summary

Our verdict is Likely pathogenic. Variant got 9 ACMG points: 10P and 1B. PM1 PP5_Very_Strong BP4

The NM_000059.4(BRCA2):​c.9082G>C​(p.Ala3028Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000411 in 1,461,518 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A3028S) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000041 (0 hom.)
• Consequence: BRCA2 NM_000059.4 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:8 U:1
• Conservation: PhyloP100: 2.66

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]

ACMG classification

Verdict is Likely_pathogenic. Variant got 9 ACMG points.

• PM1: In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 6 benign, 16 uncertain in NM_000059.4
• PP5: Variant 13-32379878-G-C is Pathogenic according to our data. Variant chr13-32379878-G-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 126199.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-32379878-G-C is described in Lovd as [Likely_benign].
• BP4: Computational evidence support a benign effect (MetaRNN=0.35421127). . Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRCA2	NM_000059.4	c.9082G>C	p.Ala3028Pro	missense_variant	23/27	ENST00000380152.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRCA2	ENST00000380152.8	c.9082G>C	p.Ala3028Pro	missense_variant	23/27	5	NM_000059.4	A2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000411 AC: 6 AN: 1461518 Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3 AN XY: 727056

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: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000540

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:8 Uncertain:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Mar 30, 2023	Observed in an individual with triple negative breast cancer and a family history of breast and/or ovarian cancer (Wong-Brown et al., 2015); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Also known as 9310G>C; This variant is associated with the following publications: (PMID: 19043619, 22228431, 12228710, 34687993, 33609447, 29884841, 27273131, 34697207, 34308104, 35665744, 35736817, 25682074) -
Likely pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Mar 01, 2024	The BRCA2 c.9082G>C (p.Ala3028Pro) variant has been reported in the published literature in individuals with breast cancer (PMIDs: 25682074 (2015) and 27273131 (2016)) or Fanconi anemia with at least one case where the variant is in trans with another BRCA2 pathogenic variant (PMIDs: 34687993 (2021), 34697207 (2022), and 36721989 (2023)). Experimental studies showed that this variant has a deleterious effect in homology-directed DNA repair assays (PMIDs: 29884841 (2019), 33609447 (2021), and 35736817 (2022)). This variant has not been reported in large, multi-ethnic general populations (Genome Aggregation Database, http://gnomad.broadinstitute.org). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded conflicting predictions that this variant is deleterious or benign. Based on the available information, this variant is classified as likely pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jun 02, 2023	This missense variant replaces alanine with proline at codon 3028 of the BRCA2 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). Functional studies have shown that this variant impacts BRCA2 function in homology-directed DNA repair assays (PMID: 29884841, 33609447, 35736817). This variant has been reported in three individuals affected with breast cancer (PMID: 25682074, 27273131, ClinVar: SCV000184056.9) and in the compound heterozygous state with c.4415_4418delAGAA in an individual affected with autosomal recessive Fanconi anemia (PMID: 34687993, 34697207). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Dec 04, 2023	The p.A3028P pathogenic mutation (also known as c.9082G>C), located in coding exon 22 of the BRCA2 gene, results from a G to C substitution at nucleotide position 9082. The alanine at codon 3028 is replaced by proline, an amino acid with highly similar properties. This alteration was found to segregate with disease in a family with early-onset breast cancer (Ambry internal data). In addition, this variant has been confirmed in trans with a pathogenic mutation in BRCA2 in an individual with a mild form of Fanconi anemia (Ip E et al. J Med Genet. 2022 Sep;59(9):912-915). This variant was non-functional in a homology-directed DNA repair (HDR) assay (Richardson ME et al. Am J Hum Genet. 2021 Mar;108(3):458-468). Internal structural analysis predicts that this alteration will disrupt single-stranded DNA binding (Ambry internal data). This amino acid position is poorly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. However, because this variant has been identified in a patient with Fanconi Anemia, this alteration may be hypomorphic, and thus, carriers of this variant and their families may present with reduced risks, and not with the typical clinical characteristics of a high-risk pathogenic BRCA2 alteration. As risk estimates are unknown at this time, clinical correlation is advised. -

Hereditary breast ovarian cancer syndrome Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 18, 2024	This sequence change replaces alanine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 3028 of the BRCA2 protein (p.Ala3028Pro). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with breast cancer or Fanconi anemia (PMID: 25682074, 27273131, 34687993, 34697207). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 126199). Advanced modeling performed at Invitae incorporating data from internal and/or published experimental studies (PMID: 33609447) indicates that this missense variant is expected to disrupt BRCA2 function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects BRCA2 function (PMID: 29884841, 33609447). RNA analysis performed to evaluate the impact of this missense change on mRNA splicing indicates it does not significantly alter splicing (Invitae). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Mar 16, 2023	Variant summary: BRCA2 c.9082G>C (p.Ala3028Pro) results in a non-conservative amino acid change located in the OB3 fold (IPR015188), which is part of the DNA-binding domain of the Brca2 protein (Hart_2019). Three of four in-silico tools predict a benign effect of the variant on protein function. The variant was absent in 249750 control chromosomes (gnomAD). c.9082G>C has been reported in the literature in individuals affected with breast cancer (Byers_2016, Wong-Brown_2015) and other tumor phenotypes (McReynolds_2021, Kim_2021). In addition, the variant was also reported in a patient diagnosed with late-onset Fanconi anaemia, who carried a pathogenic (frame-shift) variant in trans (Ip_2022), which suggests that the variant might be a hypomorphic allele. An in vitro functional study reported that this variant results in a decreased activity in homology-directed DNA repair (HDR) assay (Hart_2018, Richardson_2021, Hu_2022). Five submitters have provided clinical-significance assessments for this variant in ClinVar after 2014, partly without evidence for independent evaluation, and classified the variant as pathogenic (n=1) / likely pathogenic (n=1), or VUS (n=3). Based on the evidence outlined above, the variant was classified as likely pathogenic. -

Fanconi anemia complementation group D1 Pathogenic:1

Likely pathogenic, no assertion criteria provided

clinical testing

Molecular Medicine, NSW Health Pathology North, Newcastle

May 17, 2017

At the time it was classified as a Variant of Unknown Significance. -

Familial cancer of breast Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Feb 28, 2024

- -

Breast-ovarian cancer, familial, susceptibility to, 2 Uncertain:1

Uncertain significance, flagged submission

clinical testing

Breast Cancer Information Core (BIC) (BRCA2)

May 29, 2002

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.66
BayesDel_addAF	Uncertain	0.091	D
BayesDel_noAF	Benign	-0.11
CADD	Benign	18
DANN	Uncertain	0.99
Eigen	Benign	-0.18
Eigen_PC	Benign	-0.051
FATHMM_MKL	Uncertain	0.86	D
M_CAP	Uncertain	0.12	D
MetaRNN	Benign	0.35	T;T
MetaSVM	Benign	-0.92	T
MutationTaster	Benign	0.99	N;N
PrimateAI	Benign	0.24	T
PROVEAN	Benign	-0.69	N;N
REVEL	Uncertain	0.35
Sift	Uncertain	0.0020	D;D
Sift4G	Uncertain	0.0070	D;D
Vest4		0.44
MutPred		0.39		Loss of helix (P = 0.0033);Loss of helix (P = 0.0033);
MVP		0.88
MPC		0.13
ClinPred		0.65	D
GERP RS		3.3
gMVP		0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs80359161; hg19: chr13-32954015;