13-32396886-T-G

Position:

• chr13-32396886-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BP6_Very_Strong

The NM_000059.4(BRCA2):​c.9502-12T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000115 in 1,613,892 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 Benign (★★★).

• Frequency:
  • Genomes: 𝑓 0.00011 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00012 (0 hom.)
• Consequence: BRCA2 NM_000059.4 intron
• Scores: Splicing: ADA: 0.7178
• Clinical Significance: Benign reviewed by expert panel U:5 B:12
• Conservation: PhyloP100: 1.49

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BP6: Variant 13-32396886-T-G is Benign according to our data. Variant chr13-32396886-T-G is described in ClinVar as [Benign]. Clinvar id is 52856.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32396886-T-G is described in Lovd as [Likely_benign]. Variant chr13-32396886-T-G is described in Lovd as [Benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRCA2	NM_000059.4	c.9502-12T>G		intron_variant		ENST00000380152.8	NP_000050.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BRCA2	ENST00000380152.8	c.9502-12T>G		intron_variant		5	NM_000059.4	ENSP00000369497.3
BRCA2	ENST00000530893.7	c.9133-12T>G		intron_variant		1		ENSP00000499438.2
BRCA2	ENST00000614259.2	n.*1560-12T>G		intron_variant		2		ENSP00000506251.1

Frequencies

GnomAD3 genomes AF: 0.000105 AC: 16 AN: 152228 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0000482

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: 0.0000941

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000191

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000916 AC: 23 AN: 251114 Hom.: 0 AF XY: 0.000110 AC XY: 15 AN XY: 135750

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: 0.0000327

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000176

Gnomad OTH exome AF: 0.000327

GnomAD4 exome AF: 0.000116 AC: 170 AN: 1461664 Hom.: 0 Cov.: 31 AF XY: 0.000107 AC XY: 78 AN XY: 727152

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: 0.0000116

Gnomad4 FIN exome AF: 0.0000749

Gnomad4 NFE exome AF: 0.000146

Gnomad4 OTH exome AF: 0.0000497

GnomAD4 genome AF: 0.000105 AC: 16 AN: 152228 Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8 AN XY: 74374

Gnomad4 AFR AF: 0.0000482

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.0000941

Gnomad4 NFE AF: 0.000191

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000156 Hom.: 0

Bravo AF: 0.000125

ClinVar

Significance: Benign

Submissions summary: Uncertain:5 Benign:12

Revision: reviewed by expert panel

Submissions by phenotype

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

Benign, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA2)	Jun 21, 1999	- -
Uncertain significance, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The BRCA2 c.9502-12T>G variant was identified in 4 of 1160 proband chromosomes (frequency: 0.0034) from individuals or families with hereditary breast and ovarian cancer (Joosse 2012, Levanat 2012, Tea 2014). The variant was also identified in dbSNP (ID: rs81002803) as “With Likely benign, Uncertain significance allele,” ClinVar (as Uncertain significance by Ambry Genetics, Likely benign by Invitae and Illumina, and Benign by BIC), Clinvitae (6x), LOVD 3.0 (12x), UMD-LSDB (as likely neutral, co-occurring with a pathogenic variant BRCA2 p.Ile411AsnfsX17), and BIC Database (2x with no clinical importance). The variant was not identified in Cosmic, MutDB, ARUP Laboratories, Zhejiang Colon Cancer Database. The variant was identified in control databases in 33 of 276870 chromosomes at a frequency of 0.000119 (Genome Aggregation Consortium Feb 27, 2017). The variant was also identified by our laboratory in 10 individuals with breast cancer. The literature shows conflicting evidence regarding the pathogenicity of this variant. Based on mRNA studies, the variant has been shown to result in the loss of a splice acceptor site and deletion of exon 26 (Joosse 2012, Vehmanen 1997, Walker 2013). However, another study by Acedo (2015) showed the variant produced weak effects, with less than 15% of abnormal isoforms, thus stating the variants role in breast cancer is questionable but it might constitute a low-penetrance or disease-modifier allele. In addition, statistical analyses by Houdayer (2012) and Pruss (2014) determined that the variant had no splicing effect. The c.9502-12T>G variant is located in the 3' splice region but does not affect the invariant -1 and -2 positions. However, positions -3 and -5 to -12 are part of the splicing consensus sequence and variants involving these positions sometimes affect splicing. In addition, 1 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing; this is not very 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. -
Benign, reviewed by expert panel	curation	Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)	Jun 18, 2019	IARC class based on posterior probability from multifactorial likelihood analysis, thresholds for class as per Plon et al. 2008 (PMID: 18951446). Class 1 based on posterior probability = 4.00E-07 -
Benign, no assertion criteria provided	clinical testing	Department of Medical and Surgical Sciences, University of Bologna	Sep 01, 2023	BS1(Strong)+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) -
Uncertain significance, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Mar 06, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -

not specified Uncertain:1 Benign:2

Benign, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Aug 15, 2023	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Aug 01, 2019	- -
Benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Mar 22, 2021	Variant summary: BRCA2 c.9502-12T>G alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 4/4 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 9.1e-05 in 251630 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in BRCA2 causing Hereditary Breast And Ovarian Cancer Syndrome (9.1e-05 vs 0.00075), allowing no conclusion about variant significance. c.9502-12T>G has been reported in the literature in individuals affected with breast/ovarian cancer (example, Houdayer_2012, Joosse_2012, Vehmanen_1997, Tea_2014, Levanat_2012, Wong-Brown_2015). These report(s) do not provide unequivocal conclusions about association of the variant with Hereditary Breast and Ovarian Cancer. At-least one co-occurrence with another pathogenic variant has been reported in the UMD database (BRCA2 c.1232_1242delinsACAT, p.Ile411AsnfsX17), providing supporting evidence for a benign role. Several publications report experimental evidence demonstrating no splicing impact of this variant utilizing stabilized RNA extracted from lymphoblastoid cell lines and in minigene assays (example, Acedo_2015, Houdayer_2012 and Wangensteen_2019). Although at-least one study has demonstrated a partial effect on splicing reporting a skipping of exon 26, the physiological consequences of which are unknown (Leman_2018). Multiple clinical diagnostic laboratories and an expert panel (ENIGMA) have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Multiple submitters reported the variant with conflicting assessments (benign, n=3, likely benign, n=1, VUS, n=5) of whom the expert panel has assessed the variant as benign. Due to the lack of any evidence supporting an actionable outcome in over five years of evaluations at our laboratory, further supported by the emerging consensus among peers as outlined above, the variant was classified as benign. -

Hereditary cancer-predisposing syndrome Benign:3

Likely benign, criteria provided, single submitter	clinical testing	Ambry Genetics	Jan 16, 2020	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. -
Benign, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Apr 29, 2016	- -
Likely benign, criteria provided, single submitter	curation	Sema4, Sema4	Mar 31, 2021	- -

Hereditary breast ovarian cancer syndrome Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	clinical testing	Mendelics	Aug 22, 2023	- -

Fanconi anemia complementation group D1 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Mar 06, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -

not provided Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

GeneDx

Nov 05, 2018

This variant is denoted BRCA2 c.9502-12T>G or IVS25-12T>G and consists of a T>G nucleotide substitution at the -12 position of intron 25 of the BRCA2 gene. In silico analysis, which includes splice predictors and evolutionary conservation, supports a deleterious effect. While an mRNA analysis suggested this variant causes loss of the nearby splice acceptor site, leading to deletion of exon 26 and a non-functional protein (Joosse 2012), an RT-PCR mini-gene assay detected only weak effects on splicing (Acedo 2015). This variant, also denoted as 9730-12T>G using alternate nomenclature, has been observed in at least four individuals with a personal or family history of breast and/or ovarian cancer (Vehmanen 1997, Levanat 2012, Tea 2014, Wong-Brown 2015). BRCA2 c.9502-12T>G was also seen in a breast tumor, which was determined to have characteristics similar to BRCA2-associated tumors (Joosse 2012). This variant was observed at an allele frequency of 0.02% (28/126,428) in individuals of European ancestry in large population cohorts (Lek 2016). Based on currently available evidence, it is unclear whether BRCA2 c.9502-12T>G is a pathogenic or benign variant. We consider it to be a variant of uncertain significance. -

BRCA2-related disorder Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Sep 28, 2023

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Familial cancer of breast Benign:1

Benign, criteria provided, single submitter

clinical testing

Genetics and Molecular Pathology, SA Pathology

Oct 12, 2020

The BRCA2 c.9502-12T>G variant is classified as Benign (BS3, BP4, BP6) Well established functional studies do not support a deleterious effect of this variant (BS3). Functional studies reported in the literature indicate aberrant splicing results from this variant (Joosse et al., 2010 PMID:20614180), and was confirmed by our laboratory in 2015. However independent studies demonstrate the abnormal transcripts are expressed at a very low level (8%) below that expected to effect haploinsufficiency (Houdayer et al., 2012 PMID:22505045, Acedo et al., 2015 PMID: 25382762) Multiple lines of computational evidence suggest this variant has no impact on the gene or gene product (BP4). Functional studies for this variant are inconsistent in their conclusions. RNA studies performed by our laboratory in 2015 indicate that BRCA2:c.9502-12T>G does effect abnormal splicing, however clinical importance of the transcribed mRNA variants remains uncertain. Joosse et al., 2010 (PMID:20614180) demonstrated that this variant led to the deletion of exon 26 and results in non-functional proteins. However, Houdayer et al., 2012 (PMID: 22505045) recorded that the observed consequence of BRCA2:c.9502-12T>G was ‘no change’. Finally, Acedo et al., 2015 (PMID: 25382762) used a minigene assay to demonstrate that this variant results in very low level of exon 26 skipping (8%). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	15
DANN	Benign	0.65

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.72
dbscSNV1_RF	Benign	0.50
SpliceAI score (max)		0.020		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: rs81002803; hg19: chr13-32971023; COSMIC: COSV104700966; COSMIC: COSV104700966;