13-32319100-T-G

Position:

• chr13-32319100-T-G

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1 PM2 PM5

The NM_000059.4(BRCA2):​c.91T>G​(p.Trp31Gly) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. W31C) has been classified as Likely pathogenic.

• Frequency: Genomes: not found (cov: 33)
• Consequence: BRCA2 NM_000059.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1 U:4
• Conservation: PhyloP100: 5.67

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 6 ACMG points.

• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 3 benign, 16 uncertain in NM_000059.4
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr13-32319101-G-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 2098802.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRCA2	NM_000059.4	c.91T>G	p.Trp31Gly	missense_variant	3/27	ENST00000380152.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRCA2	ENST00000380152.8	c.91T>G	p.Trp31Gly	missense_variant	3/27	5	NM_000059.4	A2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1 Uncertain:4

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Malignant tumor of breast Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Aug 28, 2023

Variant summary: BRCA2 c.91T>G (p.Trp31Gly) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 250830 control chromosomes (gnomAD). c.91T>G has been reported in the literature, primarily as a VUS in settings of multigene panel testing in individuals affected with breast cancer, most with a family history of HBOC-related and/or other cancers (e.g. Ikeda_2001, Chan_2018, Caleca_2018, Shao_2020, El Ansari_2020). These reports do not necessarily provide unequivocal conclusions about association of the variant with breast cancer or HBOC. Several publications report experimental evidence evaluating an impact on protein function. These studies found that the variant impaired the interaction between BRCA2 and PALB2 (Caleca_2018), was unable to rescue the lethal cell phenotype in an mESC functional complementation assay (Thomassen_2022), and support a damaging effect of this variant on homology directed repair (HDR capacity) based on a high throughput cell based viability assay (MANO-B method) to evaluate drug sensitivity of BRCA2 variants treated with PARP inhibitors (olaparib, niraparib, rucaparib and carboplatin) at various concentrations (Ikegami_2020). The following publications have been ascertained in the context of this evaluation (PMID: 30410870, 30093976, 32778078, 11149425, 32444794, 31742824, 35979650). Three submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as likely pathogenic. -

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

Uncertain significance, criteria provided, single submitter

clinical testing

All of Us Research Program, National Institutes of Health

Jun 08, 2023

This missense variant replaces tryptophan with glycine at codon 31 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 has poor complementation in Brca2-deficient mouse embryonic stem cells and demonstrates sensitivity to PARP inhibitors (PMID: 32444794, 35979650). This variant has been reported in individuals affected with early-onset breast cancer and ovarian cancer (PMID: 30093976, 30410870, 32778078). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Different variants affecting the same codon, c.91T>C (p.Trp31Arg) and c.92G>C (p.Trp31Ser), are considered to be pathogenic (ClinVar Variation ID: 52775, 2098802), suggesting that Trp at this position is important for BRCA2 protein function. The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -

not provided Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Quest Diagnostics Nichols Institute San Juan Capistrano

Jul 12, 2021

- -

Hereditary cancer-predisposing syndrome Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Dec 01, 2022

The p.W31G variant (also known as c.91T>G), located in coding exon 2 of the BRCA2 gene, results from a T to G substitution at nucleotide position 91. The tryptophan at codon 31 is replaced by glycine, an amino acid with highly dissimilar properties. This variant has been reported in multiple breast cancer families in the literature (Chan GHJ et al. Oncotarget, 2018 Jul;9:30649-30660; Caleca L et al. Front Oncol, 2018 Oct;8:480; Shao D et al. Cancer Sci., 2020 Feb;111:647-657; El Ansari FZ et al. BMC Cancer, 2020 Aug;20:747). This alteration was also reported to abrogate the BRCA2-PALB2 protein binding based on an in vitro assay specifically designed to test the BRCA2-PALB2 interaction (Caleca L et al. Front Oncol, 2018 Oct;8:480). This alteration was non-functional in a cell-survival-based drug sensitivity assay compared to wildtype (Ikegami M et al. Nat Commun, 2020 May;11:2573). In a mouse embryonic stem cell assay this variant led to poor cell viability and the authors noted that the tryptophan residue at codon 31 may be a critical residue for BRCA2PALB2 interaction (Thomassen M et al. Hum Mutat, 2022 Aug). This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -

Hereditary breast ovarian cancer syndrome Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Invitae

Sep 04, 2023

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. This variant disrupts the p.Trp31 amino acid residue in BRCA2. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 9537232, 16793542, 18363094, 19609323, 20215541, 21939546, 22194698, 22678057, 24285729). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Experimental studies have shown that this missense change affects BRCA2 function (PMID: 30410870). 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. ClinVar contains an entry for this variant (Variation ID: 481540). This missense change has been observed in individual(s) with breast cancer and/or ovarian cancer (PMID: 30093976, 30410870, 31742824). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces tryptophan, which is neutral and slightly polar, with glycine, which is neutral and non-polar, at codon 31 of the BRCA2 protein (p.Trp31Gly). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.86
BayesDel_addAF	Uncertain	0.083	D
BayesDel_noAF	Benign	-0.12
CADD	Uncertain	24
DANN	Uncertain	0.98
Eigen	Pathogenic	0.73
Eigen_PC	Pathogenic	0.72
FATHMM_MKL	Uncertain	0.96	D
M_CAP	Uncertain	0.13	D
MetaRNN	Uncertain	0.73	D;D
MetaSVM	Benign	-1.2	T
MutationTaster	Benign	1.0	D;D
PrimateAI	Uncertain	0.63	T
PROVEAN	Uncertain	-3.3	D;D
REVEL	Uncertain	0.36
Sift	Pathogenic	0.0	D;D
Sift4G	Pathogenic	0.0	D;D
Vest4		0.64
MutPred		0.59		Gain of disorder (P = 0.0087);Gain of disorder (P = 0.0087);
MVP		0.88
MPC		0.15
ClinPred		0.99	D
GERP RS		5.7
gMVP		0.76

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: rs80359182; hg19: chr13-32893237;