rs397507404

Positions:

• chr13-32370955-G-A
• chr13-32370955-G-C
• chr13-32370955-G-T

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_000059.4(BRCA2):​c.8488-1G>A variant causes a splice acceptor, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,766 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000027 (0 hom.)
• Consequence: BRCA2 NM_000059.4 splice_acceptor, intron
• Scores: Splicing: ADA: 0.9999
• Clinical Significance: Pathogenic reviewed by expert panel P:27
• Conservation: PhyloP100: 9.32

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 Pathogenic. Variant got 18 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift change.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 13-32370955-G-A is Pathogenic according to our data. Variant chr13-32370955-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 38164.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32370955-G-A is described in Lovd as [Pathogenic]. Variant chr13-32370955-G-A is described in Lovd as [Likely_pathogenic]. Variant chr13-32370955-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.8488-1G>A		splice_acceptor_variant, intron_variant		ENST00000380152.8	NP_000050.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BRCA2	ENST00000380152.8	c.8488-1G>A		splice_acceptor_variant, intron_variant		5	NM_000059.4	ENSP00000369497.3
BRCA2	ENST00000530893.7	c.8119-1G>A		splice_acceptor_variant, intron_variant		1		ENSP00000499438.2
BRCA2	ENST00000614259.2	n.*546-1G>A		splice_acceptor_variant, intron_variant		2		ENSP00000506251.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000274 AC: 4 AN: 1461766 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 727186

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000447

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 8.99e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000756

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:27

Revision: reviewed by expert panel

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 2 Pathogenic:9

Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Oct 31, 2023	- -
Likely pathogenic, no assertion criteria provided	clinical testing	Sharing Clinical Reports Project (SCRP)	Sep 23, 2011	- -
Pathogenic, criteria provided, single submitter	research	HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology	Feb 11, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -
Pathogenic, 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 5 based on posterior probability = 0.992712 -
Pathogenic, criteria provided, single submitter	clinical testing	Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge	Oct 02, 2015	- -
Pathogenic, criteria provided, single submitter	research	Laan Lab, Human Genetics Research Group, University of Tartu	May 01, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Counsyl	Mar 09, 2015	- -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein	Aug 23, 2021	ACMG classification criteria: PVS1 very strong, PS3 supporting, PS4 moderate, PM2 moderate -

not provided Pathogenic:5

Pathogenic, no assertion criteria provided	research	Gharavi Laboratory, Columbia University	Sep 16, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	May 26, 2022	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Aug 05, 2022	PP3, PP5, PM2, PS3_moderate, PVS1_moderate -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Dec 04, 2024	Observed in multiple individuals with personal and/or family histories consistent with Hereditary Breast and Ovarian Cancer (PMID: 22632462, 22798144, 24607278, 24916970, 27741520, 27383479, 29673794, 30606148, 30350268); Reported in the homozygous state in an individual with Fanconi anemia that was described as mild, whose lympohoblasts exhibited modest MMC sensitivity; as well as a second individual with non-obstructive azoospermia (PMID: 12065746, 35535697); Published functional studies are inconclusive: marginal sensitivity to PARP inhibitor and other DNA damaging agents and wild type levels of RAD51 foci formation (PMID: 25583207); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on splicing; Also known as 8716-1G>A; This variant is associated with the following publications: (PMID: 24916970, 24301060, 28726806, 29446198, 26247049, 29907814, 27383479, 26834852, 25382762, 24259538, 28332257, 16115142, 25447315, 27741520, 15645491, 22798144, 19464302, 29673794, 25525159, 22632462, 24607278, 29625052, 26580448, 30606148, 30350268, 30078507, 28111427, 29790872, 31131967, 33008098, 31447099, 33397043, 31589614, 28888541, 32986223, 34235180, 34413315, 35535697, 32719484, 34645131, 35264596, 36988593, 36451132, 34326862, 33309985, 33087929, 35534704, 12065746, 36881271, 36721989, 37118955, 38671360, 25583207) -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Nov 10, 2021	This variant disrupts a canonical splice-acceptor site and interferes with normal BRCA2 mRNA splicing (PMIDs: 22632462 (2012), 24607278 (2014)). In the published literature, the variant has been reported in individuals with Fanconi anemia (PMID: 12065746 (2002)) and with breast/ovarian cancer (PMIDs: 24607278 (2014), 30078507 (2018), 30606148 (2019)). It has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). Based on the available information, this variant is classified as pathogenic. -

Hereditary breast ovarian cancer syndrome Pathogenic:5

Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jan 06, 2021	The c.8488-1G>A variant in BRCA2 has been reported in the heterozygous state in at least 8 individuals with BRCA2-related cancers, and in the homozygous state in 1 individual with Fanconi anemia (Acedo 2012 PMID: 22632462, Santos 2014 PMID: 24607278, Park 2017 PMID: 28111427, Li 2018 PMID: 30078507 , Palmero 2018 PMID: 29907814, Cotrim 2019 PMID: 30606148). This variant has also been reported by other clinical laboratories in ClinVar (Variation ID: 38164) and was absent from large population studies. This variant occurs within the canonical splice site (+/- 1,2) and is predicted to cause altered splicing leading to an abnormal or absent protein. Sequencing of patient RNA confirms that this variant leads to abnormal splicing (Howlett 2002 PMID: 12065746, Acedo 2012 PMID: 22632462, Santos 2014 PMID: 24607278). In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant hereditary breast and ovarian cancer (HBOC). ACMG/AMP Criteria applied: PVS1, PM2_Supporting, PS4_Moderate. -
Pathogenic, criteria provided, single submitter	clinical testing	Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine	Jul 05, 2018	The c.8488-1G>A variant in the BRCA2 gene is located at the canonical acceptor splice site of intron 19. It is predicted to result in acceptor loss (SpliceAI delta score: 0.92) and aberrant splicing and disrupted protein product. The variant has been reported in multiple individuals with breast/ovarian/prostate cancer (PMID: 35264596, 37118955, 30350268, 22798144, 34235180). This variant has also been reported in homozygosity in an individual affected with Fanconi anemia (PMID: 12065746). Experimental RNA analysis in patient lymphocytes and minigene assay have shown that this variant may cause aberrant transcripts (PMID: 22632462, 12065746, 24607278). Loss-of-function variants of BRCA2 are known to be pathogenic (PMID: 8988179, 11897832, 29446198). The variant is reported in ClinVar as pathogenic (ID:38164) and reviewed by the expert panel. The variant is absent in the general population database (gnomAD). Therefore, the c.8488-1G>A variant in the BRCA2 gene has been classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Oct 19, 2020	Variant summary: BRCA2 c.8488-1G>A is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Two predict that the variant abolishes a 3' acceptor site. Several publications report experimental evidence that this variant affects mRNA splicing (e.g. Acedo_2012, Santos_2014). The variant was absent in 251414 control chromosomes. c.8488-1G>A has been reported in the literature in individuals affected with Hereditary Breast And Ovarian Cancer Syndrome (e.g. Acedo_2012, Kim_2012, Peixoto_2014, Fernandes_2016) and Fanconi anemia (e.g. Howlett_2002). These data indicate that the variant is likely to be associated with disease.Several publications report experimental evidence evaluating an impact on protein function, indicating that the variant impairs protein function (e.g. Howlett_2002, Godthelp_2006). 13 other clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2023	This sequence change affects an acceptor splice site in intron 19 of the BRCA2 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in BRCA2 are known to be pathogenic (PMID: 20104584). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with breast cancer, autosomal recessive Fanconi anemia (PMID: 22632462, 24301060, 24607278, 27741520, 31331294). This variant is also known as Ex19-1G>A, IVS19-1G>A. ClinVar contains an entry for this variant (Variation ID: 38164). 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: 12065746). Studies have shown that this variant is associated with altered splicing resulting in multiple RNA products ( PMID: 22632462, 24607278, 25382762; Invitae). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, no assertion criteria provided	research	Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto	Jan 31, 2014	- -

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jan 09, 2023	This variant causes a G>A nucleotide substitution at the canonical -1 position of intron 19 splice acceptor site of the BRCA2 gene. This variant is also known as IVS19-1G>A in the literature. RNA studies have shown that this variant results in several different abnormally spliced transcripts, including a transcript missing 12 nucleotides of exon 20, a transcript that retains intron 19, and another transcript with exon 20 skipping (PMID: 12065746, 22632462, 24607278, 25382762; ClinVar SCV000278235.5). Functional studies have shown that the mutant protein results in a decreased number of cells with RAD51 foci and reduced focus size, confers a moderate defect in homologous recombination, and disrupts replication fork protection function (PMID: 32354836). This variant has been observed in over ten individuals affected with breast and/or ovarian cancer (PMID: 22632462, 22798144, 24916970, 27741520, 33008098; Chheda 2020, DOI: 10.4103/CRST.CRST_1; Color data) and in an individual affected with colorectal cancer with family history of breast cancer (PMID: 33309985). This variant has also been reported in a homozygous individual affected with a mild form of Fanconi anemia (PMID: 12065746), and cells derived from this individual showed a modest sensitivity to a DNA damaging agent, suggesting that this variant may be hypomorphic in some individuals. This variant has not been identified 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 Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Oct 15, 2024	The c.8488-1G>A intronic pathogenic mutation results from a G to A substitution one nucleotide upstream from coding exon 19 of the BRCA2 gene. This mutation was previously reported in a homozygous state in one Fanconi anemia patient of subtype D1 with a family history of consanguinity (Howlett NG et al. Science. 2002 Jul;26:297(5581):606-9). Results from various functional splicing assays performed on this alteration demonstrated that this mutation results in three to five different abnormally spliced transcripts, which includes production of an abnormal transcript that loses 12 nucleotides of exon 20, a transcript that retains intron 19, and another transcript with exon 20 skipping (Acedo et al. Breast Cancer Res. 2012 May; 25:14(3):R87; Santos C et al. J. Mol. Diagn. 2014 May;16(3):324-34; Acedo et al Hum. Mutat. 2015 Feb;36(2):210-21; Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). In addition to the clinical data presented in the literature, alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as a disease-causing mutation. However, because this variant is identified in one or more patients with Fanconi Anemia it may be 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. -

Medulloblastoma;C0346153:Familial cancer of breast;C0376358:Malignant tumor of prostate;C1838457:Fanconi anemia complementation group D1;C2675520:Breast-ovarian cancer, familial, susceptibility to, 2;C2751641:Glioma susceptibility 3;C3150546:Pancreatic cancer, susceptibility to, 2;CN033288:Wilms tumor 1 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Oct 31, 2018

- -

Fanconi anemia complementation group D1 Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Jul 26, 2002

- -

BRCA2-related cancer predisposition Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

All of Us Research Program, National Institutes of Health

Sep 02, 2024

This variant causes a G>A nucleotide substitution at the canonical -1 position of intron 19 splice acceptor site of the BRCA2 gene. This variant is also known as IVS19-1G>A in the literature. RNA studies have shown that this variant results in several different abnormally spliced transcripts, including a transcript missing 12 nucleotides of exon 20, a transcript that retains intron 19, and another transcript with exon 20 skipping (PMID: 12065746, 22632462, 24607278, 25382762; ClinVar SCV000278235.5). Functional studies have shown that the mutant protein results in a decreased number of cells with RAD51 foci and reduced focus size, confers a moderate defect in homologous recombination, and disrupts replication fork protection function (PMID: 32354836). This variant has been observed in over ten individuals affected with breast and/or ovarian cancer (PMID: 22632462, 22798144, 24916970, 27741520, 33008098; Chheda 2020, DOI: 10.4103/CRST.CRST_1; Color data) and in an individual affected with colorectal cancer with family history of breast cancer (PMID: 33309985). This variant has also been reported in a homozygous individual affected with a mild form of Fanconi anemia (PMID: 12065746), and cells derived from this individual showed a modest sensitivity to a DNA damaging agent, suggesting that this variant may be hypomorphic in some individuals. This variant has not been identified 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 Pathogenic. -

BRCA2-related disorder Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

DASA

Apr 10, 2022

The c.8488-1G>A variant is located in a canonical splice-site, and it is predicted to alter gene function due to either exon skipping or nonsense-mediate decay – NMD, and the variant is present in a relevant exon to the transcript - PVS1. This sequence change has been observed in affected individual(s) and ClinVar contains an entry for this variant (ClinVar ID: 38164; PMID: 22632462; PMID: 24607278; PMID: 27741520; PMID: 25382762; PMID: 22632462) - PS4. This variant is not present in population databases (rs397507404- gnomAD; ABraOM no frequency - http://abraom.ib.usp.br) - PM2. In summary, the currently available evidence indicates that the variant is pathogenic -

Gastric cancer Pathogenic:1

Pathogenic, no assertion criteria provided

research

Laboratory for Genotyping Development, RIKEN

Jul 01, 2021

- -

Familial cancer of breast Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Mar 09, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.38	D
BayesDel_noAF	Pathogenic	0.31
CADD	Pathogenic	34
DANN	Uncertain	0.99
Eigen	Pathogenic	1.2
Eigen_PC	Pathogenic	1.0
FATHMM_MKL	Pathogenic	0.99	D
GERP RS		5.1

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.89
SpliceAI score (max)		0.92		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.37		Position offset: 13
DS_AL_spliceai		0.92		Position offset: 1

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

Publications

LitVar

Other links and lift over

dbSNP: rs397507404; hg19: chr13-32945092; COSMIC: COSV104430719; COSMIC: COSV104430719;