13-32357808-T-C

Position:

• chr13-32357808-T-C

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2 PP3_Strong

The NM_000059.4(BRCA2):​c.7684T>C​(p.Phe2562Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,613,828 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.000020 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: BRCA2 NM_000059.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1 U:10 B:1
• Conservation: PhyloP100: 7.45

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.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.977

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRCA2	NM_000059.4	c.7684T>C	p.Phe2562Leu	missense_variant	16/27	ENST00000380152.8	NP_000050.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BRCA2	ENST00000380152.8	c.7684T>C	p.Phe2562Leu	missense_variant	16/27	5	NM_000059.4	ENSP00000369497	A2

Frequencies

GnomAD3 genomes AF: 0.0000197 AC: 3 AN: 152206 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000441

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1461622 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 727138

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: 0.00000180

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0000197 AC: 3 AN: 152206 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 74366

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000441

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000507 Hom.: 0

Bravo AF: 0.0000227

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1 Uncertain:10 Benign:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 2 Uncertain:3 Benign:1

Likely benign, no assertion criteria provided	clinical testing	Sharing Clinical Reports Project (SCRP)	Sep 27, 2010	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Counsyl	Apr 09, 2018	- -
Uncertain significance, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Oct 06, 2023	This missense variant replaces phenylalanine with leucine at codon 2562 of the BRCA2 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Functional studies have shown that this variant to be defective in a homology-directed DNA repair assay (PMID: 29394989, 30696104). This variant has been reported in an individual at risk for hereditary breast and ovarian cancer (PMID: 27062684). This variant also has been reported with a pathogenic BRCA2 covariant in a cell line from an individual affected with Fanconi anemia, although the phasing of the two variants is unknown (PMID: 25583207). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). 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. -
Uncertain significance, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA2)	Nov 25, 2004	- -

not provided Pathogenic:1 Uncertain:1

Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Oct 18, 2024	Published functional studies demonstrate defective or intermediate impact on homology-directed repair (HDR) activity and reduced binding to DSS1 (PMID: 29394989, 30696104, 29884841, 35665744); Identified in at least one family with breast and/or ovarian cancer (PMID: 27062684); 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 7912T>C; This variant is associated with the following publications: (PMID: 19043619, 17452773, 25348012, 30696104, 29884841, 35665744, 29394989, 12228710, 27062684, 25583207) -
Uncertain significance, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Aug 26, 2020	- -

Hereditary cancer-predisposing syndrome Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Sep 14, 2023	This missense variant replaces phenylalanine with leucine at codon 2562 of the BRCA2 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Functional studies have shown that this variant to be defective in a homology-directed DNA repair assay (PMID: 29394989, 30696104). This variant has been reported in an individual at risk for hereditary breast and ovarian cancer (PMID: 27062684). This variant also has been reported with a pathogenic BRCA2 covariant in a cell line from an individual affected with Fanconi anemia, although the phasing of the two variants is unknown (PMID: 25583207). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). 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. -
Uncertain significance, criteria provided, single submitter	clinical testing	Ambry Genetics	Aug 15, 2023	The p.F2562L variant (also known as c.7684T>C), located in coding exon 15 of the BRCA2 gene, results from a T to C substitution at nucleotide position 7684. The phenylalanine at codon 2562 is replaced by leucine, an amino acid with highly similar properties. This alteration co-occurs with a pathogenic BRCA2 frameshift mutation in a cell line derived from a Fanconi Anemia patient; however, the phase of these two alterations was not described (Stoepker C et al. DNA Repair (Amst.), 2015 Feb;26:54-64). One homology directed repair (HDR) assay found this alteration to be defective (Guidugli L et al. Am. J. Hum. Genet., 2018 Jan;:), while another HDR assay found this alteration to have intermediate function (Hart SN et al. Genet Med, 2019 01;21:71-80). In a study of 1854 high-risk breast/ovarian cancer families in Italy, this alteration was detected in 1 family (Azzollini J et al. Eur J Intern Med, 2016 Jul;32:65-71).This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is conflicting at this time, the clinical significance of this alteration remains unclear. -

Hereditary breast ovarian cancer syndrome Uncertain:2

Uncertain significance, criteria provided, single submitter	curation	Cancer Variant Interpretation Group UK, Institute of Cancer Research, London	Dec 11, 2023	Data used in classification: The frequency of this variant is 0/138,632 individuals in gnomAD (PM2_mod). The variant is in the DNA-binding domain of BRCA2 (PM1_sup). December 2023 Update: Functional assay data has since been made available (Hart et al., 2019, PMID: 29884841) which supersedes the previously applied Guidugli et al., 2018 assay results. The new data shows an intermediate result, therefore, this functional assay data is no longer applicable towards pathogenicity. Data not used in classification: There are conflicting in silico predictions; AlignGVGD (class: C15), SIFT (Deleterious), Polyphen2 HumVar (probably damaging) and CADD (27.2). -
Uncertain significance, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 26, 2024	This sequence change replaces phenylalanine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 2562 of the BRCA2 protein (p.Phe2562Leu). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with breast cancer, Fanconi anemia, and/or ovarian cancer (PMID: 25583207, 27062684). ClinVar contains an entry for this variant (Variation ID: 38114). 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%. Experimental studies have shown that this missense change affects BRCA2 function (PMID: 29394989, 30696104). 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. -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

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

Oct 16, 2023

Variant summary: BRCA2 c.7684T>C (p.Phe2562Leu) results in a non-conservative amino acid change located in the Breast cancer type 2 susceptibility protein, helical domain of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251286 control chromosomes. c.7684T>C has been reported in the literature in individuals affected with Hereditary Breast And Ovarian Cancer Syndrome or Fanconi Anemia (Stoepker_2015, Azzollini_2016). These reports do not provide unequivocal conclusions about association of the variant with Hereditary Breast And Ovarian Cancer Syndrome. At least one publication reports experimental evidence evaluating an impact on protein function and showed that this variant decreased the BRCA2 function (Guidugli_2018, Hart_2019, Caleca_2019, Biswas_2020). The following publications have been ascertained in the context of this evaluation (PMID: 27062684, 33293522, 30696104, 29394989, 29884841, 25583207). Seven submitters have cited clinical-significance assessments for this variant to ClinVar after 2014 (VUS n=6, likely pathogenic n=1). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic. -

BRCA2-related disorder Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Aug 20, 2024

The BRCA2 c.7684T>C variant is predicted to result in the amino acid substitution p.Phe2562Leu. This variant has been reported in an individual with hereditary breast and/or ovarian cancer (Azzollini et al. 2016. PubMed ID: 27062684). It has also been reported along with a second pathogenic variant in a lymphoblastoid cell line in an individual with Fanconi anemia; however confirmation of phase of the two variants was not determined (Stoepker et al. 2014. PubMed ID: 25583207). Functional studies report conflicting results in that some indicate a detrimental effect on protein function and viability (Biswas et al. 2020. PubMed ID: 33293522; Caleca et al. 2019. PubMed ID: 30696104), where other studies suggest a neutral or intermediate effect on protein function (Hart et al. 2018. PubMed ID: 29884841; Karchin et al. 2008. PubMed ID: 19043619). This variant is not present in a large population database, indicating this is rare. It has conflicting classifications in ClinVar, ranging from likely benign to uncertain (https://www.ncbi.nlm.nih.gov/clinvar/variation/38114/). An alternate nucleotide change affecting the same amino acid has been reported in an individual with clinical features consistent with Fanconi anemia (Internal Data, PreventionGenetics). Although we suspect that this variant may be pathogenic, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.95
BayesDel_addAF	Pathogenic	0.37	D
BayesDel_noAF	Pathogenic	0.29
CADD	Pathogenic	27
DANN	Uncertain	1.0
Eigen	Pathogenic	0.79
Eigen_PC	Pathogenic	0.70
FATHMM_MKL	Pathogenic	0.98	D
M_CAP	Pathogenic	0.49	D
MetaRNN	Pathogenic	0.98	D;D
MetaSVM	Pathogenic	1.1	D
MutationTaster	Benign	1.0	D;D
PrimateAI	Uncertain	0.60	T
PROVEAN	Benign	-1.8	N;N
REVEL	Pathogenic	0.88
Sift	Pathogenic	0.0	D;D
Sift4G	Pathogenic	0.0	D;D
Vest4		0.78
MutPred		0.88		Gain of helix (P = 0.0696);Gain of helix (P = 0.0696);
MVP		0.97
MPC		0.17
ClinPred		1.0	D
GERP RS		5.2
gMVP		0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.10		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: rs80358995; hg19: chr13-32931945;