rs80359165

chr13-32379900-A-Cchr13-32379900-A-Gchr13-32379900-A-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM1

The NM_000059.4(BRCA2):c.9104A>C(p.Tyr3035Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000645 in 1,613,654 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. Y3035C) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.000033 (0 hom., cov: 33)
  • Exomes 𝑓: 0.000068 (0 hom.)
• Consequence: BRCA2 NM_000059.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:7 B:10 O:1
• Conservation: PhyloP100: 2.75

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 Uncertain_significance. Variant got 2 ACMG points.

• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 6 benign, 14 uncertain in NM_000059.4

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRCA2	NM_000059.4	c.9104A>C	p.Tyr3035Ser	missense_variant	23/27	ENST00000380152.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRCA2	ENST00000380152.8	c.9104A>C	p.Tyr3035Ser	missense_variant	23/27	5	NM_000059.4	A2

Frequencies

GnomAD3 genomes AF: 0.0000328 AC: 5 AN: 152272 Hom.: 0 Cov.: 33

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: 0.0000735

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000481 AC: 12 AN: 249232 Hom.: 0 AF XY: 0.0000297 AC XY: 4 AN XY: 134844

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000290

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: 0.0000980

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000677 AC: 99 AN: 1461382 Hom.: 0 Cov.: 32 AF XY: 0.0000647 AC XY: 47 AN XY: 726974

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000224

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: 0.0000873

Gnomad4 OTH exome AF: 0.0000166

GnomAD4 genome AF: 0.0000328 AC: 5 AN: 152272 Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4 AN XY: 74400

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: 0.0000735

Gnomad4 OTH AF: 0.00

Bravo AF: 0.0000340

TwinsUK AF: 0.000270 AC: 1

ALSPAC AF: 0.00 AC: 0

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000116 AC: 1

ExAC AF: 0.0000494 AC: 6

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:7 Benign:10 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

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

Uncertain significance, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA2)	May 29, 2002	- -
Benign, no assertion criteria provided	clinical testing	Sharing Clinical Reports Project (SCRP)	Aug 18, 2011	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	Sep 21, 2015	- -
Benign, no assertion criteria provided	clinical testing	Department of Medical and Surgical Sciences, University of Bologna	Sep 01, 2023	BS1(Supporting)+BP4(Supporting)+BP5(Very Strong) according to ACMG/AMP classification guidelines specified for BRCA1 & BRCA2 (Classification Criteria V1.0.0 2023-09-08 - https://cspec.genome.network/cspec/ui/svi/affiliation/50087) (PMID: 38160042) -

not provided Benign:4

Likely benign, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Apr 12, 2023	- -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Feb 01, 2021	In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 27221827, 10923033, 24728327, 25782689, 25971625, 20104584, 18627636, 19043619, 23231788, 26183948, 27616075, 28324225, 28283652, 21952622, 22711857, 21673748, 22476429, 29394989, 29088781, 24094589, 20167696, 29341116, 29988080, 30254663, 28726806, 29684080, 31409081, 31300551, 31294896, 32444794, 31131967, 31954625, 32123317, 29884841) -
Likely benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Apr 27, 2023	- -
Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jan 01, 2024	BRCA2: BP1, BP2, BS3:Supporting -

Hereditary cancer-predisposing syndrome Uncertain:1 Benign:2

Uncertain significance, criteria provided, single submitter	curation	Sema4, Sema4	Dec 05, 2021	- -
Likely benign, criteria provided, single submitter	clinical testing	Ambry Genetics	Dec 07, 2018	This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Likely benign, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Oct 28, 2015	- -

Breast and/or ovarian cancer Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	Jan 06, 2020	- -
Uncertain significance, no assertion criteria provided	clinical testing	Foulkes Cancer Genetics LDI, Lady Davis Institute for Medical Research	Oct 11, 2013	- -

Hereditary breast ovarian cancer syndrome Uncertain:1 Benign:1

Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	- -
Uncertain significance, no assertion criteria provided	clinical testing	Cancer Genetics and Genomics Laboratory, British Columbia Cancer Agency	Apr 14, 2016	- -

not specified Benign:1 Other:1

not provided, no classification provided	reference population	ITMI	Sep 19, 2013	- -
Benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Oct 31, 2022	Variant summary: BRCA2 c.9104A>C (p.Tyr3035Ser) results in a non-conservative amino acid change located in the DNA-binding domain (Shimelis 2017, Guidugli 2018) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 5.8e-05 in 345886 control chromosomes (gnomAD and publication data), predominantly found within the Non-Finnish European subpopulation at a frequency of 9.8e-05. This frequency is not higher than the estimated maximum expected for a pathogenic variant in BRCA2 causing Hereditary Breast and Ovarian Cancer (HBOC) Syndrome (0.00075), allowing no conclusion about variant significance. The variant, c.9104A>C, has been reported in the literature in several individuals affected with prostate cancer, breast cancer and ovarian cancer (e.g. Kote-Jarai 2011, Moghadasi 2013, Alsop 2012, Muendlein 2015, Dodova 2015, Shimelis 2017, Sadowski 2017, Alvarez 2017, Jakimovska 2018, Zuntini 2018, Fostira_2020), however it also was found in several healthy controls (e.g. Dodova 2015, Shimelis 2017). In addition, multiple co-occurrences with other pathogenic variants have been reported (BRCA1 c.2603C>G (p.Ser868X), BRCA2 c.1540_1549del (p.Glu514MetfsX8) and BRCA2 c.7913_7917delTTCCT (p.Phe2638X) in the UMD database; and BRCA2 c.5645C>A (p.Ser1882X) in Shimelis 2017), providing supporting evidence for a benign role. Several publications reported experimental evidence evaluating an impact on protein function, and demonstrated no effect on splicing (Thery_2011, Wai_2020), and a mild impact on BRCA2 protein function, representing an activity comparable to wild-type, or a somewhat hypomorphic allele (e.g. Shimelis 2017, Guidugli 2018, Mesman 2018, Ikegami_2020). One case-control study found that this variant was associated with moderately increased risks of breast cancer for Caucasian women (odds ratio (OR) = 2.52; P = 0.04), and while the number of cases and controls with the Y3035S variant were relatively small, this moderate risk estimate was supported by family pedigree analysis, showing partial co-segregation with breast cancer (Shimelis 2017). On the other hand, in a recent large study evaluating breast cancer cases and controls in the Breast Cancer Association Consortium (BCAC), the variant was reported in 12/60466 cases, and in 7/53461 controls (Dorling 2021 through LOVD), indicating a much lower odds ratio that is well below the OR of BRCA2 truncations (5.85 [95% CI: 4.85-7.06]) or pathogenic BRCA2 missense variants (5.68 [95% CI: 2.62 to 12.29]) reported in this study (Dorling 2021). In addition, multifactorial probability models, performing systematic assessments of variants of unknown significance in the BRCA genes, which included analysis of co-occurrence in trans with known deleterious mutations, personal and family history of cancer, tumor pathology and co-segregation with disease in pedigrees, predicted this variant to be (likely) neutral (Parsons 2019, Caputo 2021). Nine other clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation, and reported the variant with conflicting assessments (benign, n=1; likely benign, n=4; VUS, n=4). Based on the evidence outlined above, the variant of interest represents a neutral- or mildly hypomorphic variant, however, it is not a high penetrance causative variant within the settings of inherited Hereditary Breast and Ovarian Cancer Syndrome. Therefore, the variant was classified as benign. -

Malignant tumor of breast Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

-

The BRCA2 p.Tyr3035Ser variant was identified in 28 of 105,838 proband chromosomes (frequency: 0.0003) from individuals or families with prostate and hereditary breast and ovarian cancer and was present in 8 of 98,938 control chromosomes (frequency: 0.00008) from healthy individuals (Moghadasi 2013, Kote-Jarai 2011, Alsop 2012, Dodova 2015, Muendlein 2015, Kraus 2017, Meisel 2017, Shimelis 2017). The variant was identified in dbSNP (rs80359165) as “with uncertain significance, other allele”, ClinVar (classified as uncertain significance by GeneDx, Integrated Genetics BIC, Sinai Health System and 4 other submitters, likely benign by Ambry Genetics, Color and Invitae and benign by SCRP), LOVD 3.0 (observed 27x) and UMD-LSDB (observed 19x). The variant was identified in control databases in 14 of 280,642 chromosomes at a frequency of 0.00005 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: European in 13 of 127,670 chromosomes (freq: 0.0001), Latino in 1 of 35,294 chromosomes (freq: 0.00003), while the variant was not observed in the African, Ashkenazi Jewish, East Asian, Finnish, Other and South Asian populations. The variant co-segregated with disease in multiple high-risk breast cancer families (Shimelis 2017). In UMD-LSDB, the variant was observed in samples with co-occurring pathogenic BRCA2 (c.1540_1549del p.Glu514Metfs*8, c.7913_7917delTTCCT p.Phe2638*) and BRCA1 (c.2603C>G p.Ser868*) variants. In one study, in vitro expression of the variant altered homology directed repair activity and decreased BRCA2 DNA binding (Shimelis 2017). The p.Tyr3035 residue is conserved in mammals but not in more distantly related organisms, and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the variant may impact the protein; however, this information is not predictive enough to assume pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.90
BayesDel_addAF	Uncertain	0.061	T
BayesDel_noAF	Uncertain	0.070
Cadd	Uncertain	24
Dann	Uncertain	0.99
Eigen	Uncertain	0.60
Eigen_PC	Uncertain	0.54
FATHMM_MKL	Uncertain	0.93	D
M_CAP	Pathogenic	0.29	D
MetaRNN	Uncertain	0.65	D;D
MetaSVM	Uncertain	0.18	D
MutationTaster	Benign	0.99	D;D
PrimateAI	Uncertain	0.50	T
PROVEAN	Uncertain	-2.4	N;N
REVEL	Pathogenic	0.67
Sift	Pathogenic	0.0	D;D
Sift4G	Pathogenic	0.0010	D;D
Vest4		0.57
MVP		0.90
MPC		0.18
ClinPred		0.52	D
GERP RS		4.5
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: rs80359165; hg19: chr13-32954037;