chr13-32344558-G-T

Position:

• chr13-32344558-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP3

The NM_000059.4(BRCA2):​c.6842G>T​(p.Gly2281Val) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00000147 in 1,357,750 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000015 (0 hom.)
• Consequence: BRCA2 NM_000059.4 missense, splice_region
• Scores: Splicing: ADA: 0.9999
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:6 B:1
• Conservation: PhyloP100: 3.70

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]

BRCA2 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.789

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRCA2	NM_000059.4	c.6842G>T	p.Gly2281Val	missense_variant, splice_region_variant	12/27	ENST00000380152.8	NP_000050.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BRCA2	ENST00000380152.8	c.6842G>T	p.Gly2281Val	missense_variant, splice_region_variant	12/27	5	NM_000059.4	ENSP00000369497.3
BRCA2	ENST00000530893.7	c.6473G>T	p.Gly2158Val	missense_variant, splice_region_variant	12/27	1		ENSP00000499438.2
BRCA2	ENST00000614259.2	n.6842G>T		splice_region_variant, non_coding_transcript_exon_variant	11/26	2		ENSP00000506251.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000147 AC: 2 AN: 1357750 Hom.: 0 Cov.: 25 AF XY: 0.00000147 AC XY: 1 AN XY: 680324

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: 0.0000121

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.79e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

EpiCase AF: 0.0000547

EpiControl AF: 0.0000593

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:6 Benign:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

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

Uncertain significance, criteria provided, single submitter	clinical testing	Counsyl	Apr 14, 2016	- -
Uncertain significance, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA2)	May 29, 2002	- -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

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

Apr 10, 2021

Variant summary: BRCA2 c.6842G>T (p.Gly2281Val) alters the first conserved nucleotide of exon 12 and results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. Several computational tools predict a significant impact on normal splicing: Three predict the variant weakens the adjacent canonical 3' acceptor site. Two predict the variant strengthens a cryptic exonic alternate 3' acceptor site. Although these specific predictions have not been confirmed by published functional studies, several studies have reported that this variant results in a complete in-frame skipping of exon 12 (example, Grodeck_2014, Meulmans_2020). The variant was absent in 244980 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.6842G>T has been reported in the literature in one individual affected with Hereditary Breast And Ovarian Cancer (example, Meulmans_2020). This report does not provide unequivocal conclusions about association of the variant with Hereditary Breast And Ovarian Cancer Syndrome. At-least four co-occurrences with another pathogenic variant have been reported in the BIC database, the literature and at our laboratory (BRCA2 c.9196C>T, p.Gln3066*, BIC database; BRCA2 c.9195_9196delinsAT, p.Phe3065_Gln3066delinsLeuTer, our laboratory and Meulmans_2020) providing supporting evidence for a benign role. These co-occurrences are suggestive of this variant occuring in cis with c.9195_9196delinsAT. At least two publications report experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in >50%-90% of normal homology directed repair (HDR) activity in mouse embryonic stem cell based assays of BRCA2 variants that affect exon 12 splicing (example, Meulmans_2020, Biswas_2020). The functional studies are consistent with reports of an in-frame exon 12 skipped BRCA2 isoform that is expressed in normal blood and breast tissues. Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as uncertain significance. Some submitters cite overlapping evidence utilized in the context of this evaluation. Based on the evidence outlined above, the variant was classified as uncertain significance. -

not provided Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Quest Diagnostics Nichols Institute San Juan Capistrano

Nov 14, 2019

- -

Hereditary cancer-predisposing syndrome Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Mar 09, 2022

The p.G2281V variant (also known as c.6842G>T) is located in coding exon 11 of the BRCA2 gene. The glycine at codon 2281 is replaced by valine, an amino acid with dissimilar properties. This change occurs in the first base pair of coding exon 11 which makes it likely to have some effect on normal mRNA splicing. In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site. This alteration has been shown to result in skipping of coding exon 11 (Also known as Exon 12 in the literature-Ambry internal data; Hujová P et al. Mol. Biol. Rep., 2019 Jun;46:2877-2884; Grodecká L et al. PLoS One. 2014 Feb 21;9(2):e89570; Hujová P et al. Mol. Biol. Rep. 2019 Jun;46(3):2877-2884; Meulemans L et al. Cancer Res., 2020 Apr;80:1374-1386). The loss of coding exon 11 has intermediate effects on homology-directed DNA repair activity; however, the clinical impacts of this intermediate function are not yet clear (Meulemans L et al. Cancer Res., 2020 Apr;80:1374-1386). This alteration was reported as functional in a mouse embryonic stem cell survival and drug sensitivity assay (Biswas K. et al. NPJ Genom Med. 2020 Dec;5(1):52). A different variant that results in incomplete coding exon 11 skipping was identified in compound heterozygous state in a patient without apparent Fanconi Anemia suggesting exon 12 skipping is dispensable for clinically relevant function at a certain threshold (Meulemans L et al. Cancer Res., 2020 Apr;80:1374-1386; Li L et al. Hum. Mutat., 2009 Nov;30:1543-50). This amino acid position is highly conserved in available vertebrate species. In addition, the protein 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

Labcorp Genetics (formerly Invitae), Labcorp

Oct 04, 2023

This sequence change replaces glycine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 2281 of the BRCA2 protein (p.Gly2281Val). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with breast and ovarian cancer (PMID: 32046981). ClinVar contains an entry for this variant (Variation ID: 52212). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Studies have shown this missense change is associated with skipping of exon 12, but one or more of the resulting mRNA isoform(s) may be naturally occurring (PMID: 24586880; Invitae). 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. -

Familial cancer of breast Benign:1

Likely benign, criteria provided, single submitter

clinical testing

MGZ Medical Genetics Center

Feb 09, 2024

ACMG codes applied following ENIGMA VCEP rules: BS3, BP2, PM2_SUP -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.20
BayesDel_addAF	Pathogenic	0.24	D
BayesDel_noAF	Uncertain	0.10
CADD	Uncertain	25
DANN	Uncertain	1.0
Eigen	Uncertain	0.65
Eigen_PC	Uncertain	0.59
FATHMM_MKL	Uncertain	0.97	D
M_CAP	Pathogenic	0.51	D
MetaRNN	Pathogenic	0.79	D;D
MetaSVM	Uncertain	0.44	D
PrimateAI	Benign	0.37	T
PROVEAN	Benign	-2.1	N;N
REVEL	Pathogenic	0.65
Sift	Pathogenic	0.0	D;D
Sift4G	Uncertain	0.0030	D;D
Vest4		0.53
MutPred		0.51		Gain of sheet (P = 0.0344);Gain of sheet (P = 0.0344);
MVP		0.95
MPC		0.18
ClinPred		0.99	D
GERP RS		5.0
gMVP		0.33

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.98
SpliceAI score (max)		0.92		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.92		Position offset: 0

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

Publications

LitVar

Other links and lift over

dbSNP: rs80358908; hg19: chr13-32918695;