13-32379745-A-G

Position:

• chr13-32379745-A-G

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM2 PP3 PP5_Very_Strong

The NM_000059.4(BRCA2):​c.8954-5A>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: BRCA2 NM_000059.4 splice_region, splice_polypyrimidine_tract, intron
• Scores: Splicing: ADA: 0.9985
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:14
• Conservation: PhyloP100: 3.23

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 11 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 13-32379745-A-G is Pathogenic according to our data. Variant chr13-32379745-A-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 267712.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-32379745-A-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRCA2	NM_000059.4	c.8954-5A>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	c.8954-5A>G		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		5	NM_000059.4	ENSP00000369497	A2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:14

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:4

Likely pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Oct 16, 2018	Not found in the total gnomAD dataset, and the data is high quality (0/276278 chr). Found in at least one symptomatic patient. Predicted to negatively affect a known splice site. Nucleotide conservation is uninformative. Assessment of experimental evidence suggests this variant results in abnormal protein function. -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Oct 28, 2019	Non-canonical splice site variant demonstrated to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease (Menendez 2012, de Garibay 2014 Santos 2014, Baert 2017); Observed in individuals with personal and family history consistent with HBOC (de Juan Jimenez 2013, Santos 2014, Peixoto 2015); Not observed in large population cohorts (Lek 2016); Also known as 9182-5A>G; This variant is associated with the following publications: (PMID: 26187060, 24916970, 23479189, 31131967, 30702160, 30415210, 21735045, 24607278, 24123850, 29280214) -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	Oct 23, 2020	- -
Pathogenic, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	- -

Hereditary breast ovarian cancer syndrome Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 22, 2024	This sequence change falls in intron 22 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 not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with breast cancer and/or hereditary breast and ovarian cancer (PMID: 21735045, 23479189, 24123850, 24607278, 24916970, 30702160). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 267712). Studies have shown that this variant alters mRNA splicing and is expected to lead to the loss of protein expression (PMID: 21735045, 24123850, 24607278; Invitae). For these reasons, this variant has been classified as Pathogenic. -
Likely pathogenic, no assertion criteria provided	research	Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto	Dec 17, 2015	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Dec 19, 2016	Variant summary: The BRCA2 c.8954-5A>G variant involves the alteration of a non-conserved intronic nucleotide. One in silico tool predicts a benign outcome for this variant. 5/5 splice prediction tools predict an alteration on normal splicing, which is confirmed by functional studies which shows the variant incudes aberrant splicing of intron 22 with the retention of its last 4 bp, which is predicted to result in out of frame product (de Garibay_2014, Menendez_2012, Santos_2014). This variant is absent in 120924 control chromosomes, but was reported in numerous affected individuals in the literature, including one family in which 1 carrier unaffected, two families with one non-carrier in each family had HBOC. These families show some level of non-segregation. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant is classified as likely pathogenic. -

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

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, no assertion criteria provided	clinical testing	BRCAlab, Lund University	Mar 02, 2020	- -

Familial cancer of breast Pathogenic:2

Likely pathogenic, no assertion criteria provided	literature only	Center for Precision Medicine, Meizhou People's Hospital	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Feb 26, 2024	Criteria applied: PVS1,PM5_STR,PM2_SUP -

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Oct 10, 2022	This variant causes an A to G nucleotide substitution at the -5 position of intron 22 of the BRCA2 gene. RNA studies found that this variant causes out-of-frame splicing of intron 22 (PMID: 21735045, 24123850, 24607278, 29280214), resulting in premature truncation. This variant has been reported in at least seven individuals affected with breast or ovarian cancer (PMID: 23479189, 24607278, 26187060, 35918668, DOI: 10.5603/OCP.2020.0026) and in families suspected of being affected with hereditary breast and ovarian cancer (PMID: 21735045, 24123850, 30415210, 33875706). 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. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Aug 21, 2023	The c.8954-5A>G intronic variant results from an A to G substitution 5 nucleotides upstream from coding exon 22 in the BRCA2 gene. This alteration has been identified in several hereditary breast cancer families, and was found to segregate with disease in one family (Menéndez M et al. Breast Cancer Res. Treat., 2012 Apr;132:979-92; Santos C et al. J Mol Diagn, 2014 May;16:324-34; de Juan Jiménez I et al. Fam. Cancer, 2013 Dec;12:767-77). 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. RT-PCR and minigene analyses determined that this alteration results in the creation of a novel splice acceptor site that causes an out of frame retention of 4 nucleotides of intron 21 (also called intron 22 in the literature) and results in a truncated mRNA transcript (Amrby internal data; Menéndez M et al. Breast Cancer Res. Treat., 2012 Apr;132:979-92; de Garibay GR et al. Hum. Mutat., 2014 Jan;35:53-7; Santos C et al. J Mol Diagn, 2014 May;16:324-34; Baert A et al. Hum. Mutat. 2018 Apr;39(4):515-526). Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

Breast-ovarian cancer, familial, susceptibility to, 1 Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Institute of Human Genetics, University of Leipzig Medical Center

Jan 27, 2023

_x000D_ Criteria applied: PS3_MOD, PS4_MOD, PM2_SUP, PP3 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	22
DANN	Benign	0.63

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.96
SpliceAI score (max)		0.85		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.85		Position offset: 1
DS_AL_spliceai		0.64		Position offset: 5

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

Publications

LitVar

Other links and lift over

dbSNP: rs886040949; hg19: chr13-32953882;