rs431825362

Positions:

• chr13-32363187-C-A
• chr13-32363187-C-G
• chr13-32363187-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_000059.4(BRCA2):​c.7985C>A​(p.Thr2662Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000185 in 1,460,966 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. T2662T) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.000018 (0 hom.)
• Consequence: BRCA2 NM_000059.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:11 B:1
• Conservation: PhyloP100: 4.75

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]

BRCA2 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.23026547).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRCA2	NM_000059.4	c.7985C>A	p.Thr2662Lys	missense_variant	18/27	ENST00000380152.8	NP_000050.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BRCA2	ENST00000380152.8	c.7985C>A	p.Thr2662Lys	missense_variant	18/27	5	NM_000059.4	ENSP00000369497.3
BRCA2	ENST00000530893.7	c.7616C>A	p.Thr2539Lys	missense_variant	18/27	1		ENSP00000499438.2
BRCA2	ENST00000614259.2	n.*43C>A		non_coding_transcript_exon_variant	17/26	2		ENSP00000506251.1
BRCA2	ENST00000614259.2	n.*43C>A		3_prime_UTR_variant	17/26	2		ENSP00000506251.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000400 AC: 1 AN: 250098 Hom.: 0 AF XY: 0.00000739 AC XY: 1 AN XY: 135322

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

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: 0.00000885

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000185 AC: 27 AN: 1460966 Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13 AN XY: 726828

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: 0.0000243

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:11 Benign:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 2 Uncertain:4

Uncertain significance, no assertion criteria provided	clinical testing	Sharing Clinical Reports Project (SCRP)	Mar 21, 2011	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Apr 02, 2016	- -
Uncertain significance, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Dec 15, 2023	This missense variant replaces threonine with lysine at codon 2662 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). Splice site prediction tools suggest that this variant may not impact RNA splicing. An RNA study has shown that the variant results in exon 18 skipping (PMID: 26845104). However, the impact on RNA splicing may be partial and the clinical relevance of this observation is not known. This variant has been reported in individuals affected with ovarian cancer (PMID: 22711857, 23633455) and colon cancer (PMID: 26845104), and a multifactorial analysis has reported co-occurrence and family history likelihood ratios for pathogenicity of 1.1022 and 0.566, respectively (PMID: 31131967). This variant has also been identified in 1/250098 chromosomes 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	Counsyl	Feb 19, 2016	- -

Hereditary cancer-predisposing syndrome Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Ambry Genetics	Aug 26, 2024	The p.T2662K variant (also known as c.7985C>A), located in coding exon 17 of the BRCA2 gene, results from a C to A substitution at nucleotide position 7985. The threonine at codon 2662 is replaced by lysine, an amino acid with similar properties. In one study, this variant was observed in 1/1001 patients with non-mucinous ovarian carcinoma and classified as a variant of uncertain significance by the authors (Alsop K et al. J Clin Oncol, 2012 Jul;30:2654-63). This alteration is predicted to alter exonic splice enhancers, and a functional RNA study showed that it leads to skipping of exon 18 (Shirts BH et al. Genet. Med., 2016 Oct;18:974-81). This alteration was also identified in an individual diagnosed with a head/neck squamous cell carcinoma (Chandrasekharappa SC et al. Cancer, 2017 Oct;123:3943-3954). This amino acid position is poorly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Based on the available evidence, the clinical significance of this variant remains unclear. -
Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Feb 01, 2023	This missense variant replaces threonine with lysine at codon 2662 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). Splice site prediction tools suggest that this variant may not impact RNA splicing. An RNA study has shown that the variant results in exon 18 skipping (PMID: 26845104). However, the impact on RNA splicing may be partial and the clinical relevance of this observation is not known. This variant has been reported in individuals affected with ovarian cancer (PMID: 22711857, 23633455) and colon cancer (PMID: 26845104), and a multifactorial analysis has reported co-occurrence and family history likelihood ratios for pathogenicity of 1.1022 and 0.566, respectively (PMID: 31131967). This variant has also been identified in 1/250098 chromosomes 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	curation	Sema4, Sema4	Nov 27, 2021	- -

not provided Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Apr 15, 2016	This variant is denoted BRCA2 c.7985C>A at the cDNA level, p.Thr2662Lys (T2662K) at the protein level, and results in the change of a Threonine to a Lysine (ACG>AAG). Using alternate nomenclature, this variant would be defined as BRCA2 8213C>A. This variant has been identified in at least one individual with epithelial ovarian cancer and at least one individual with colon cancer with a family history of pancreatic and breast cancer (Alsop 2012, Shirts 2016). Shirts et al (2016) performed RT-PCR on RNA from an affected individual and reported that this variant created an alternate transcript that skipped exon 18. However, this alternate transcript has been seen in controls and therefore, the significance of this finding is unknown (Tesoriero 2005, Walker 2010). BRCA2 Thr2662Lys was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. Since Threonine and Lysine differ in some properties, this is considered a semi-conservative amino acid substitution. BRCA2 Thr2662Lys occurs at a position that is not conserved and is located in the DNA binding and SHFM1 binding domain (Marston 1999, Yang 2002). In silico analyses predict that this variant is unlikely to alter protein structure or function. Based on currently available information, it is unclear whether BRCA2 Thr2662Lys is pathogenic or benign. We consider this to be a variant of uncertain significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	May 15, 2017	Variant summary: The BRCA2 c.7985C>A (p.Thr2662Lys) variant involves the alteration of a conserved nucleotide. 3/5 in silico tools predict a damaging outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing sites. However, ESE finder predicts that this variant may affect multiple ESE binding sites. This prediction was confirmed by RT-PCR in patient's RNA showing skipping of exon 18 (Shirts_2015), which is predicted to lead to a frameshift change. This variant has been reported in one patient with ovarian cancer and one patient with colon cancer, without strong evidence for causality. This variant is absent in 118364 control chromosomes (ExAC). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as uncertain significance except one clinical diagnostic laboratory classified this variant as pathogenic (University of Washington, Shirts_2015). Taken together, this variant is classified as a "Variant of Uncertain Significance - possibly pathogenic, until additional clinical data becomes available. -

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

Uncertain significance, criteria provided, single submitter

clinical testing

University of Washington Department of Laboratory Medicine, University of Washington

Dec 11, 2020

This variant is predicted to alter exonic splice enhancers. RT-PCR of RNA showed exon 18 skipping. Evidence from other variants that show partial skipping suggest a variable phenotype associated with exon skipping. Additional data is needed to determine the level of risk associated with this variant. -

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.Thr2662Lys variant was identified in 1 of 2924 proband chromosomes (frequency: 0.0003) from individuals or families with hereditary cancer (Shirts 2016). The variant was also identified in dbSNP (ID: rs431825362 as With Pathogenic, Uncertain significance allele) and ClinVar (7x as a variant of uncertain significance, 1x as likely pathogenic, and 1x as pathogenic). The variant was not identified in Cosmic, MutDB, LOVD 3.0, ARUP Laboratories, or Zhejiang University Database. The variant was identified in control databases in 1 of 244984 chromosomes at a frequency of 0.000004 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the European Non-Finnish population in 1 of 110928 chromosomes (freq: 0.000009) and was not observed in the African, Other, Latino, Ashkenazi Jewish, East Asian, Finnish, and South Asian populations. This variant has been shown to alter splicing of the BRCA2 transcript, resulting in the skipping of exon 18 (Shirts 2016); however, the biological significance of this splicing alteration is unclear. The p.Thr2662 residue is not conserved in mammals and computational analyses (SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact of this amino acid substitution to the protein; this information is not reliably predictive of pathogenicity. 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. -

Hereditary breast ovarian cancer syndrome Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Nov 10, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.15
BayesDel_addAF	Uncertain	0.047	T
BayesDel_noAF	Benign	-0.17
CADD	Benign	21
DANN	Uncertain	0.98
Eigen	Benign	-0.68
Eigen_PC	Benign	-0.48
FATHMM_MKL	Uncertain	0.89	D
M_CAP	Uncertain	0.17	D
MetaRNN	Benign	0.23	T;T
MetaSVM	Benign	-0.77	T
PrimateAI	Benign	0.29	T
PROVEAN	Benign	-0.40	N;N
REVEL	Uncertain	0.31
Sift	Uncertain	0.0010	D;D
Sift4G	Uncertain	0.0040	D;D
Vest4		0.27
MutPred		0.58		Loss of phosphorylation at T2662 (P = 0.0156);Loss of phosphorylation at T2662 (P = 0.0156);
MVP		0.87
MPC		0.021
ClinPred		0.47	T
GERP RS		4.9
gMVP		0.37

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs431825362; hg19: chr13-32937324;