chr13-32329440-C-G

Position:

chr13-32329440-C-G

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_ModeratePP4_ModeratePM3

This summary comes from the ClinGen Evidence Repository: The c.632-3C>G variant is an intronic variant occurring in intron 7 of the BRCA2 gene. This variant is present in gnomAD v2.1 (exomes only, non-cancer subset) or gnomAD v3.1 (non-cancer subset) but is below the ENIGMA BRCA1/2 VCEP threshold >0.00002 for BS1_Supporting (PM2_Supporting, BS1, and BA1 are not met). This variant is reported to result in aberrant mRNA splicing. RT-PCR and Mini-gene assays demonstrated that the variant impacts splicing by creating a new acceptor splice site, resulting in retention of 2bp from intron 7, which leads to a frameshift and generates a premature stop codon (PMIDs: 30883759, 32123317, 22505045). Reduced expression of aberrant transcript reported by one assay suggesting potential incomplete expression of the aberrant transcript (Ambry internal contributor). Appropriate code strength determined by comparison of results to PVS1 decision tree PVS1 (RNA) was downgraded to PVS1_Moderate (RNA). This variant has been detected in 2 siblings with phenotype consistent with BRCA2-Fanconi Anemia (FA). At least two clinical features of FA (physical features, pathology findings and cancer diagnosis ≤5yr) and confirmed chromosome breakage, are seen in these individuals. Both siblings were homozygous for the variant. Total points equated to 2 (PM3 met; PMID:25381700). Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 12.477 (based on Pathology LR=1.07; Co-occurrence LR=1.0498; Family History LR=11.107), within the thresholds for Moderate evidence towards pathogenicity (LR >4.3 & ≤18.7) (PP4_Moderate met; PMID:31131967, 31853058). In summary, this variant meets the criteria to be classified as a Likely pathogenic variant for BRCA2-related cancer predisposition based on the ACMG/AMP criteria applied as specified by the ENIGMA BRCA1/2 VCEP (PVS1_Moderate (RNA), PM3, PP4_Moderate). LINK:https://erepo.genome.network/evrepo/ui/classification/CA348611/MONDO:0012933/097

Frequency

Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

BRCA2
NM_000059.4 splice_region, splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.9999

Clinical Significance

Likely pathogenic reviewed by expert panel P:8U:2

Conservation

PhyloP100: -0.0370

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

PVS1

For more information check the summary or visit ClinGen Evidence Repository.

PM3

For more information check the summary or visit ClinGen Evidence Repository.

PP4

For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRCA2	NM_000059.4 linkuse as main transcript	c.632-3C>G		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000380152.8	NP_000050.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BRCA2	ENST00000380152.8 linkuse as main transcript	c.632-3C>G		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		5	NM_000059.4	ENSP00000369497	A2

Frequencies

GnomAD3 genomes

AF:

0.0000131

AC:

AN:

152154

Hom.:

Cov.:

show subpopulations

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:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00000411

AC:

AN:

243142

Hom.:

AF XY:

0.00

AC XY:

AN XY:

131370

show subpopulations

Gnomad AFR exome

AF:

0.0000668

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:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000139

AC:

AN:

1438228

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

716226

show subpopulations

Gnomad4 AFR exome

AF:

0.0000607

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:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0000131

AC:

AN:

152272

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.0000481

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:

0.00

Gnomad4 OTH

AF:

0.00

Bravo

AF:

0.00000378

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:8Uncertain:2

Revision: reviewed by expert panel

LINK: link

Submissions by phenotype

Hereditary cancer-predisposing syndrome

Pathogenic:2Uncertain:1

Uncertain significance, criteria provided, single submitter	clinical testing	Ambry Genetics	Nov 09, 2023	The c.632-3C>G intronic variant results from a C to G substitution 3 nucleotides upstream from coding exon 7 in the BRCA2 gene. This nucleotide position is well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site and will result in the creation or strengthening of a novel splice acceptor site. This alteration results in use of this novel cryptic acceptor site two nucleotides upstream of the native site resulting in a frameshifting transcript (Ambry internal data; Houdayer C et al. Hum. Mutat. 2012 Aug;33(8):1228-38; Fraile-Bethencourt E et al. J. Pathol., 2019 08;248:409-420). In addition, this alteration has been shown to express an in-frame transcript, known as 6q39_8 in the literature (Ambry internal data). This transcript has been shown to be able to perform homology directed repair in protein functional studies at a near wild-type level (Mesman, RLS et al. Genet Med 2020 08;22(8):1355-1365). This alteration was identified as homozygous in a fetus with features consistent with Fanconi anemia (Malric, A et al. Pediatr Blood Cancer 2015 Mar;62(3):463-70). Since supporting evidence is conflicting at this time, the clinical significance of this alteration remains unclear. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	May 19, 2020	This variant causes a C to G nucleotide substitution at the -3 position of intron 7 of the BRCA2 gene. Splice site prediction tools suggest that this variant may have a significant impact on RNA splicing. Functional RNA studies have shown that this variant causes the use of an alternative splice acceptor site 2-nucleotide upstream of the reference acceptor site, creating premature translation stop signal in the RNA transcripts (PMID: 22505045, 30883759). The aberrant transcripts are expected to result in an absent or non-functional protein product. This variant has been reported in individuals affected with breast and/or ovarian cancer (PMID: 22505045, Color internal data). In addition, a multifactorial likelihood model using health history and tumor pathology data has suggested this variant have a high probability of being pathogenic (PMID: 31131967). This variant has been identified in 1/243142 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of BRCA2 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Likely Pathogenic. -
Likely pathogenic, criteria provided, single submitter	curation	Sema4, Sema4	Sep 11, 2021	- -

not provided

Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jul 28, 2023	Non-canonical splice site variant demonstrated to result in loss-of-function (Houdayer et al., 2012; Fraile-Bethencourt et al., 2019); Multifactorial likelihood analysis suggests this variant is pathogenic (Parsons et al., 2019); Not observed at significant frequency in large population cohorts (gnomAD); Also known as 860-3C>G; This variant is associated with the following publications: (PMID: 26913838, 22505045, 29750258, 25416802, 32123317, 33466630, 30883759, 33646313, 25381700, 31131967) -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jul 01, 2022	BRCA2: PVS1, PM2, PS3:Supporting -

Breast-ovarian cancer, familial, susceptibility to, 2

Pathogenic:1

Likely pathogenic, no assertion criteria provided

clinical testing

Sharing Clinical Reports Project (SCRP)

Dec 06, 2011

- -

BRCA2-related cancer predisposition

Pathogenic:1

Likely pathogenic, reviewed by expert panel

curation

ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen

Jun 11, 2024

The c.632-3C>G variant is an intronic variant occurring in intron 7 of the BRCA2 gene. This variant is present in gnomAD v2.1 (exomes only, non-cancer subset) or gnomAD v3.1 (non-cancer subset) but is below the ENIGMA BRCA1/2 VCEP threshold >0.00002 for BS1_Supporting (PM2_Supporting, BS1, and BA1 are not met). This variant is reported to result in aberrant mRNA splicing. RT-PCR and Mini-gene assays demonstrated that the variant impacts splicing by creating a new acceptor splice site, resulting in retention of 2bp from intron 7, which leads to a frameshift and generates a premature stop codon (PMIDs: 30883759, 32123317, 22505045). Reduced expression of aberrant transcript reported by one assay suggesting potential incomplete expression of the aberrant transcript (Ambry internal contributor). Appropriate code strength determined by comparison of results to PVS1 decision tree PVS1 (RNA) was downgraded to PVS1_Moderate (RNA). This variant has been detected in 2 siblings with phenotype consistent with BRCA2-Fanconi Anemia (FA). At least two clinical features of FA (physical features, pathology findings and cancer diagnosis <=5yr) and confirmed chromosome breakage, are seen in these individuals. Both siblings were homozygous for the variant. Total points equated to 2 (PM3 met; PMID: 25381700). Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 12.477 (based on Pathology LR=1.07; Co-occurrence LR=1.0498; Family History LR=11.107), within the thresholds for Moderate evidence towards pathogenicity (LR >4.3 & <=18.7) (PP4_Moderate met; PMID: 31131967, 31853058). In summary, this variant meets the criteria to be classified as a Likely pathogenic variant for BRCA2-related cancer predisposition based on the ACMG/AMP criteria applied as specified by the ENIGMA BRCA1/2 VCEP (PVS1_Moderate (RNA), PM3, PP4_Moderate). -

Familial cancer of breast

Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Oct 10, 2022

- -

Hereditary breast ovarian cancer syndrome

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 26, 2024

This sequence change falls in intron 7 of the BRCA2 gene. It does not directly 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 present in population databases (rs568027879, gnomAD 0.007%). This variant has been observed in individual(s) with a personal and/or family history of breast and/or ovarian cancer (PMID: 22505045, 33466630, 33646313). ClinVar contains an entry for this variant (Variation ID: 219896). Based on a multifactorial likelihood algorithm using genetic, in silico, and/or statistical data, this variant has been determined to have a high probability of being pathogenic (PMID: 31131967). 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 introduction of a cryptic splice acceptor site and introduces a premature termination codon (PMID: 22505045, 30883759, 32123317; Invitae). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. -

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Quest Diagnostics Nichols Institute San Juan Capistrano

Feb 28, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Uncertain

DANN

Benign

0.63

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Pathogenic

1.0

dbscSNV1_RF

Pathogenic

0.97

SpliceAI score (max)

0.95

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.95

Position offset: 1

DS_AL_spliceai

0.77

Position offset: 3

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over