rs276174916

chr13-32379748-AGTT-AAA

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PVS1 PP5_Very_Strong

The NM_000059.4(BRCA2):c.8954-1_8955delinsAA variant causes a splice acceptor, coding sequence change. Variant has been reported in ClinVar as Pathogenic (★★★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: BRCA2 NM_000059.4 splice_acceptor, coding_sequence
• Clinical Significance: Pathogenic reviewed by expert panel P:10
• Conservation: PhyloP100: 4.16

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 Pathogenic. Variant got 16 ACMG points.

• PVS1: Splicing variant, LoF is a know mechanism of disease, Cryptic splice site detected, with MaxEntScore 4.6, offset of 29, new splice context is: tatttggcgtccatcatcAGatt. Cryptic site results in frameshift change. If cryptic site found is not functional and variant results in exon loss, it results in frameshift change.
• PP5: Variant 13-32379749-GTT-AA is Pathogenic according to our data. Variant chr13-32379749-GTT-AA is described in ClinVar as [Pathogenic]. Clinvar id is 142095.Status of the report is reviewed_by_expert_panel, 3 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRCA2	NM_000059.4	c.8954-1_8955delinsAA		splice_acceptor_variant, coding_sequence_variant	23/27	ENST00000380152.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRCA2	ENST00000380152.8	c.8954-1_8955delinsAA		splice_acceptor_variant, coding_sequence_variant	23/27	5	NM_000059.4	A2

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:10

Revision: reviewed by expert panel

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 2 Pathogenic:3

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, 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 = 0.993615 -
Pathogenic, criteria provided, single submitter	clinical testing	KCCC/NGS Laboratory, Kuwait Cancer Control Center	Aug 29, 2023	This variant, c.8954-1_8955delGTTinsAA, is a complex sequence change that affects an acceptor splice site in intron 22 of the BRCA2 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. Loss-of-function variants in BRCA2 are known to be pathogenic. The variant was absent in 250792 control chromosomes (gnomAD).This alteration has been identified in numerous individuals from breast and ovarian cancer families (PMID: 28152038, 28476184, 22632462, 19996028, 23451180, 31341520, 31131967, 33484353, 32438681). In silico splice site analysis predicts that this alteration will weaken the native splice donor site. Experimental in vitro studies variant have shown that this complex change results in exon skipping (PMID: 23451180, 22632462). For these reasons, this variant has been classified as Pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Apr 03, 2023	The c.8954-1_8955delGTTinsAA pathogenic mutation, located in intron 22/exon 23 (also known as intron 21/coding exon 22) of the BRCA2 gene, results from the deletion of 3 nucleotides (GTT) and insertion of 2 nucleotides (AA) between position c.8954-1 and c.8955 leading to the disruption of the native canonical splice acceptor site. This alteration has been identified in numerous individuals from breast and ovarian cancer families (Laitman Y. Hum Mutat. 2019 11;40(11):e1-e23.; Marchetti C. Ann Surg Oncol. 2018 Nov;25(12):3701-3708; Vietri MT. Med Oncol. 2021 Jan;38(2): 13; Lai KN. BMC Cancer. 2017 02;17(1):149; Oktay K et al. J Clin Oncol. 2010;28(2):240-4). This alteration was also classified as pathogenic in a multifactorial model of variant interpretation that incorporates co-segregation, family history, co-occurrence and tumor pathology and case-control data (Parsons MT et al. Hum Mutat . 2019 Sep;40(9):1557-1578). In silico splice site analysis predicts that this alteration will weaken the native splice donor site. Multiple RNA studies have shown that this alteration leads primarily to a transcript with a 51 nucleotide deletion in coding exon 22 (also called exon 23 in the literature: Ambry internal data; Acedo A et al. Breast Cancer Res. 2012;14(3):R87). The resulting transcript is expected to produce a protein with an in-frame loss of 17 amino acids. Based on internal structural analysis, this protein, V2985_T3001del, is expected to be deleterious as it is strongly untolerated and is more untolerated than remote pathogenic variants and benign variants (Ambry internal data). Furthermore, functional studies with this a peptide containing this deletion show it has impaired binding to DSS1 and single-stranded DNA (Colombo M et al. PLoS One. 2013;8(2):e57173). Of note, this alteration is also referred to as IVS22-1del3insAA and IVS22-1delGTTinsAA in published literature. 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 pathogenic. -
Pathogenic, criteria provided, single submitter	curation	Sema4, Sema4	Nov 13, 2021	- -

Familial cancer of breast Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Aug 11, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	KCCC/NGS Laboratory, Kuwait Cancer Control Center	Sep 13, 2023	This variant, c.8954-1_8955delGTTinsAA, is a complex sequence change that affects an acceptor splice site in intron 22 of the BRCA2 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. Loss-of-function variants in BRCA2 are known to be pathogenic. The variant was absent in 250792 control chromosomes (gnomAD).This alteration has been identified in numerous individuals from breast and ovarian cancer families (PMID: 28152038, 28476184, 22632462, 19996028, 23451180, 31341520, 31131967, 33484353, 32438681). In silico splice site analysis predicts that this alteration will weaken the native splice donor site. Experimental in vitro studies variant have shown that this complex change results in exon skipping (PMID: 23451180, 22632462). For these reasons, this variant has been classified as Pathogenic. -

Hereditary breast ovarian cancer syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Feb 06, 2017	This variant, c.8954-1_8955delGTTinsAA, is a complex sequence change that affects an acceptor splice site in intron 22 of the BRCA2 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. Loss-of-function variants in BRCA2 are known to be pathogenic. This particular variant has been reported in the literature in an individual affected with occult primary ovarian insufficiency (PMID: 19996028). Experimental in vitro studies variant have shown that this complex change results in skipping of exon 23 (PMID: 23451180, 22632462). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Dec 24, 2019	Variant summary: BRCA2 c.8954-1_8955delinsAA 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: Four predict the variant abolishes a 3' acceptor site. Experimental evidence support these predictions indicating the variant results in various aberrant transcripts, with the main one being a deletion of 51 nucleotides at the 5'-end of exon 23 with consequent 17-amino acids loss, which was demonstrated to abrogate the ability of BRCA2 to bind the DSS1 protein and its affinity for ssDNA (Acedo_2012, Colombo_2013). The variant was absent in 250792 control chromosomes (gnomAD). c.8954-1_8955delinsAA has been reported in the literature in individuals affected with Hereditary Breast and Ovarian Cancer (e.g. Arvai_2019, Marchetti_2018, Oktay_2010, Rebbeck_2018). These data indicate that the variant is likely to be associated with disease. Four ClinVar submitters (evaluation after 2014) cite the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Jun 20, 2022

Canonical splice site variant predicted to result in a null allele in a gene for which loss of function is a known mechanism of disease (Acedo 2012, Colombo 2013); Observed in individuals with a personal and/or family history consistent with pathogenic variants in this gene and other cancers in published literature (Oktay 2010, Johnson 2017, Santonocito 2020, Vietri 2021); Multifactorial likelihood analysis suggests this variant is pathogenic (Parsons 2019); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; Not observed at significant frequency in large population cohorts (gnomAD); Also known as 9182-1_9183delGTTinsAA; This variant is associated with the following publications: (PMID: 28152038, 28476184, 22632462, 19996028, 23451180, 31341520, 31131967, 33484353, 32438681) -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs276174916; hg19: chr13-32953886;