13-32326499-G-T

Variant names:

• chr13-32326499-G-T
• rs397507768
• NM_000059.4:c.517G>T

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2 PM5 PP3 PP5

The NM_000059.4(BRCA2):​c.517G>T​(p.Gly173Cys) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000069 in 1,449,710 control chromosomes in the GnomAD database, with no homozygous occurrence. 2/3 splice prediction tools predicting alterations to normal splicing. 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. G173R) has been classified as Pathogenic.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: BRCA2 NM_000059.4 missense, splice_region
• Scores: Splicing: ADA: 0.9979
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:2 U:3
• Conservation: PhyloP100: 2.04

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
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr13-32326499-G-C is described in Lovd as [Pathogenic].
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. Scorers claiming Uncertain: max_spliceai. No scorers claiming Benign.
• PP5: Variant 13-32326499-G-T is Pathogenic according to our data. Variant chr13-32326499-G-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 51805.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=2, Uncertain_significance=2}. Variant chr13-32326499-G-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRCA2	NM_000059.4	c.517G>T	p.Gly173Cys	missense_variant, splice_region_variant	Exon 7 of 27	ENST00000380152.8	NP_000050.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRCA2	ENST00000380152.8	c.517G>T	p.Gly173Cys	missense_variant, splice_region_variant	Exon 7 of 27	5	NM_000059.4	ENSP00000369497.3
BRCA2	ENST00000530893.7	c.148G>T	p.Gly50Cys	missense_variant, splice_region_variant	Exon 7 of 27	1		ENSP00000499438.2
BRCA2	ENST00000614259.2	n.517G>T		splice_region_variant, non_coding_transcript_exon_variant	Exon 6 of 26	2		ENSP00000506251.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 6.90e-7 AC: 1 AN: 1449710 Hom.: 0 Cov.: 30 AF XY: 0.00000139 AC XY: 1 AN XY: 721970

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000253

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:2 Uncertain:3

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Hereditary cancer-predisposing syndrome Pathogenic:2

Jun 14, 2024

Color Diagnostics, LLC DBA Color Health

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant substitutes a conserved guanine nucleotide with thymine at the first nucleotide of exon 7 in the BRCA1 gene, replacing glycine with cysteine at codon 173 of the BRCA2 protein. Computational prediction tools suggest that this variant weakens the intron 6 splice acceptor site (PMID: 35449021). Minigene RNA splicing assays have shown that this variant causes the out-of-frame splicing of exon 7, which is expected to result in an absent or non-functional protein product (PMID: 22962691, 30883759). A different variant occurring at the same nucleotide position, c.517G>C, has been shown to affect RNA splicing in carrier derived RNA (PMID: 29280214). This variant has been reported in multiple individuals affected with breast or ovarian cancer (PMID: 22962691, 25777348, 28947987, 34072659; Color internal data; UMD database). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic. -

Dec 15, 2023

Ambry Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.517G>T variant (also known as p.G173C) is located in coding exon 6 of the BRCA2 gene. The glycine at codon 173 is replaced by cysteine, an amino acid with highly dissimilar properties. This change occurs in the first base pair of coding exon 6. This alteration has been observed in multiple breast and/or ovarian cancer cohorts from multiple ethnic backgrounds (Solano AR et al. Oncotarget, 2017 Sep;8:60487-60495; El Saghir NS et al. Oncologist, 2015 Apr;20:357-64; Kang E et al. Breast Cancer Res Treat, 2015 May;151:157-68). This nucleotide and amino acid position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration may weaken the native splice acceptor site. This alteration results in complete coding exon 6 skipping (also known as Exon 7 in the literature) in multiple minigene assays (Gaildrat P et al. J. Med. Genet. 2012 Oct;49:609-17; Fraile-Bethencourt E et al. J Pathol, 2019 08;248:409-420). Another alteration impacting the same nucleotide position (c.517G>C) also causes the same splice defect (Ambry internal data; Baert A et al. Hum. Mutat. 2017 Dec). Yet another close-match alteration at this same acceptor site, BRCA2 c.517-2A>G, has been identified in a compound heterozygous and homozygous state in patients with Fanconi Anemia (Leach M et al. Practical Flow Cytometry in Hematology: 100 worked examples. 321-324; 2015; Muramatsu H et al. Genet. Med., 2017 07;19:796-802). BRCA2 c.517-2A>G also demonstrates an intermediate effect in a mouse embryonic stem cell survival and subsequent homology-directed DNA repair assays. Clinical and functional data collectively support BRCA2 c.517-2A>G as a likely hypomorphic variant (Mesman RLS et al. Genet Med, 2020 08;22:1355-1365). BRCA2 c.517-2A>G has a similar splice defect as this variant (Ambry internal data; Houdayer C et al. Hum Mut. 2012; 33:1228–38; Fraile-Bethencourt E et al. J. Pathol. 2019 08;248(4):409-420). Based on the majority of available evidence to date, this variant is likely to be pathogenic. However, because a variant with a similar splicing profile as this variant is functionally hypomorphic and has been identified in multiple patients with Fanconi Anemia it may be similarly hypomorphic and thus, carriers of this variant and their families may present with reduced risks, and not with the typical clinical characteristics of a high-risk pathogenic BRCA2 alteration. As risk estimates are unknown at this time, clinical correlation is advised. -

not specified Uncertain:1

Dec 30, 2016

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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

Feb 26, 2013

Sharing Clinical Reports Project (SCRP)

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Hereditary breast ovarian cancer syndrome Uncertain:1

Jun 27, 2023

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This missense change has been observed in individual(s) with breast cancer (PMID: 22962691, 25777348, 28947987). 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. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this missense change alters mRNA splicing and is expected to lead to the loss of protein expression (PMID: 30883759). 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. ClinVar contains an entry for this variant (Variation ID: 51805). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glycine, which is neutral and non-polar, with cysteine, which is neutral and slightly polar, at codon 173 of the BRCA2 protein (p.Gly173Cys). It affects a nucleotide within the consensus splice site. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.21
BayesDel_addAF	Uncertain	0.014	T
BayesDel_noAF	Benign	-0.22
CADD	Uncertain	24
DANN	Uncertain	1.0
Eigen	Uncertain	0.49
Eigen_PC	Uncertain	0.43
FATHMM_MKL	Uncertain	0.93	D
M_CAP	Benign	0.022	T
MetaRNN	Uncertain	0.48	T;T
MetaSVM	Benign	-0.90	T
PrimateAI	Benign	0.43	T
PROVEAN	Benign	-1.7	N;N
REVEL	Benign	0.092
Sift	Uncertain	0.0010	D;D
Sift4G	Benign	0.070	T;T
Vest4		0.44
MutPred		0.28		Loss of helix (P = 0.079);Loss of helix (P = 0.079);
MVP		0.92
MPC		0.17
ClinPred		0.92	D
GERP RS		4.6
gMVP		0.22

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.90
SpliceAI score (max)		0.40		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.40		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: rs397507768; hg19: chr13-32900636;