rs80359790

Positions:

• chr13-32326282-G-A
• chr13-32326282-G-C
• chr13-32326282-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP5

The NM_000059.4(BRCA2):​c.516G>A​(p.Lys172Lys) variant causes a splice region, synonymous change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign 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: 33)
• Consequence: BRCA2 NM_000059.4 splice_region, synonymous
• Scores: Splicing: ADA: 0.9996
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:10 U:3
• Conservation: PhyloP100: 3.71

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
• PP5: Variant 13-32326282-G-A is Pathogenic according to our data. Variant chr13-32326282-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 51795.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=2, Pathogenic=3, Likely_pathogenic=6}. Variant chr13-32326282-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRCA2	NM_000059.4	c.516G>A	p.Lys172Lys	splice_region_variant, synonymous_variant	6/27	ENST00000380152.8	NP_000050.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BRCA2	ENST00000380152.8	c.516G>A	p.Lys172Lys	splice_region_variant, synonymous_variant	6/27	5	NM_000059.4	ENSP00000369497.3
BRCA2	ENST00000530893.7	c.147G>A	p.Lys49Lys	splice_region_variant, synonymous_variant	6/27	1		ENSP00000499438.2
BRCA2	ENST00000614259.2	n.516G>A		splice_region_variant, non_coding_transcript_exon_variant	5/26	2		ENSP00000506251.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:10 Uncertain:3

Revision: criteria provided, conflicting classifications

Submissions by phenotype

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

Likely pathogenic, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Dec 14, 2023	The c.516G>A (p.Lys172=) synonymous variant in the BRCA2 gene is located at exon 6 and is predicted to inflict donor loss (SpliceAI delta score: 0.84), resulting in alternative splicing and disrupted protein product. The variant has been reported in 4 unrelated individuals with breast/ovarian/urothelial cancer (PMID: 19267246, 35464868, 31263571). Patient RNA analysis and mini gene assay showed abnormal splicing that led to nonsense-mediated decay (PMID: 19267246). The variant is absent in the general population database (gnomAD). Therefore, the c.516G>A (p.Lys172=) variant of BRCA2 has been classified as likely pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge	Oct 02, 2015	- -
Uncertain significance, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA2)	Oct 29, 2001	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet	May 27, 2024	PP1; PVS1_Strong; PM2_Supporting -

Hereditary breast ovarian cancer syndrome Pathogenic:3 Uncertain:1

Uncertain significance, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Nov 07, 2021	This sequence change affects codon 172 of the BRCA2 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the BRCA2 protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with breast and ovarian cancer and/or urothelial cancer (PMID: 19267246, 31263571). ClinVar contains an entry for this variant (Variation ID: 51795). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of exon 6 and/or exons 5-6 and introduces a premature termination codon (PMID: 19267246). The resulting mRNA is expected to undergo nonsense-mediated decay. 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. -
Pathogenic, no assertion criteria provided	clinical testing	Cancer Genomics Lab, PINUM Cancer Hospital	May 23, 2022	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jun 19, 2020	The p.Lys172Lys variant in BRCA2 has been identified in one individual with breast cancer (Hansen 2009 PubMed: 19267246) and was absent from large population studies. Exon trapping and RT-PCR analysis showed that this variant results in skipping of exon 6 and of exon 5 and 6. The skipping results in a frameshift and a premature termination at codon 154 (skipping of exon 5 and 6) or codon 168 (skipping of exon 6), which most likely will result in nonsense-mediated mRNA decay (NMD) (Hansen 2009 PubMed: 19267246). In summary, although additional studies are required to fully establish its clinical significance, this variant is likely pathogenic. ACMG/AMP Criteria applied: PM2; PS3. -
Pathogenic, criteria provided, single submitter	clinical testing	National Health Laboratory Service, Universitas Academic Hospital and University of the Free State	Nov 16, 2021	- -

not provided Pathogenic:2 Uncertain:1

Pathogenic, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Feb 06, 2024	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics Laboratory, Skane University Hospital Lund	May 27, 2022	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Mar 18, 2021	- -

Familial cancer of breast Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Mar 24, 2024

- -

Hereditary cancer-predisposing syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Dec 16, 2022

The c.516G>A variant (also known as p.K172K), located in coding exon 5 of the BRCA2 gene, results from a G to A substitution at nucleotide position 516. This nucleotide substitution does not change the at codon 172. This alteration was identified in a Danish patient with breast cancer diagnosed at 37 and 65 years old; her family history was significant for male breast cancer in her father and ovarian cancer in a paternal aunt (Hansen TV et al. Breast Cancer Res. Treat. 2010 Feb;119:547-50). This alteration was detected in a patient with urothelial cancer (Bertelsen B et al. NPJ Genom Med, 2019 Jun;4:13). This alteration was also identified in a large, worldwide study of BRCA1/2 mutation positive families (Rebbeck TR et al. Hum Mutat, 2018 05;39:593-620). However, this change occurs in the last base pair of coding exon 5, which makes it likely to have some effect on normal mRNA splicing. Splicing assays have shown this variant to result in nonsense-mediated decay prone transcripts that lack coding exons 4 and 5 (Ambry internal data; Hansen TV et al. Breast Cancer Res. Treat. 2010 Feb;119:547-50). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Uncertain	23
DANN	Benign	0.82
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	1.0
SpliceAI score (max)		0.84		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.84		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: rs80359790; hg19: chr13-32900419;