chr13-32329496-A-G

Variant names:

• chr13-32329496-A-G
• rs397507884
• NM_000059.4:c.681+4A>G

Variant summary

Our verdict is Pathogenic. The variant received 15 ACMG points: 15P and 0B. PS3 PM2 PP3 PP5_Very_Strong

The NM_000059.4(BRCA2):​c.681+4A>G variant causes a splice region, 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 (★★). ClinVar reports functional evidence for this variant: "SCV000661243: Splicing studies from both human lymphoblastoid cell lines and minigene show that this variant results in use of the predicted alternate donor site leading to a frameshift with predicted premature truncation (Houdayer C et al. Hum. Mutat., 2012 Aug;33:1228-38; Fraile-Bethencourt E et al. J. Pathol., 2019 Aug;248:409-420).; SCV001358249: This variant may cause an intronic cryptic donor be used which inserted 4 nucleotides downstream from 5′ splice site shown in RNA extracted from patient derived lymphoblastoid cell lines and minigene assay (PMID:22505045, 30883759).; SCV000694998: "These predictions were confirmed by experimental evidence demonstrating the variant to improve an intronic cryptic donor site resulting in the insertion of 4 nucleotides which causes a frameshift (p.N228Vfs*11) (Fraile-Bethencourt_2019, Houdayer_2012)."; SCV001484289: Studies have shown that this variant alters mRNA splicing and is expected to lead to the loss of protein expression (PMID:22505045, 30883759).; SCV005624516: Splicing studies predict an alternate donor site leads to a frameshift with premature truncation, resulting in loss of protein expression (PMIDs:30883759 (2019), 26913838 (2016), and 22505045 (2012)).".

• Frequency: Genomes: not found (cov: 32)
• Consequence: BRCA2 NM_000059.4 splice_region, intron
• Scores: Splicing: ADA: 0.9968
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:6
• Conservation: PhyloP100: 2.64
• Publications: 3 publications found

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 Gene-Disease associations (from GenCC):

• BRCA2-related cancer predisposition

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• breast-ovarian cancer, familial, susceptibility to, 2

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
• Fanconi anemia complementation group D1

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), ClinGen, Ambry Genetics
• pancreatic cancer, susceptibility to, 2

  Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
• sarcoma

  Inheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
• hereditary breast ovarian cancer syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• Fanconi anemia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• medulloblastoma

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Pathogenic. The variant received 15 ACMG points.

• PS3: PS3 evidence extracted from ClinVar submissions: SCV000661243: Splicing studies from both human lymphoblastoid cell lines and minigene show that this variant results in use of the predicted alternate donor site leading to a frameshift with predicted premature truncation (Houdayer C et al. Hum. Mutat., 2012 Aug;33:1228-38; Fraile-Bethencourt E et al. J. Pathol., 2019 Aug;248:409-420).; SCV001358249: This variant may cause an intronic cryptic donor be used which inserted 4 nucleotides downstream from 5′ splice site shown in RNA extracted from patient derived lymphoblastoid cell lines and minigene assay (PMID: 22505045, 30883759).; SCV000694998: "These predictions were confirmed by experimental evidence demonstrating the variant to improve an intronic cryptic donor site resulting in the insertion of 4 nucleotides which causes a frameshift (p.N228Vfs*11) (Fraile-Bethencourt_2019, Houdayer_2012)."; SCV001484289: Studies have shown that this variant alters mRNA splicing and is expected to lead to the loss of protein expression (PMID: 22505045, 30883759).; SCV005624516: Splicing studies predict an alternate donor site leads to a frameshift with premature truncation, resulting in loss of protein expression (PMIDs:30883759 (2019), 26913838 (2016), and 22505045 (2012)).
• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing predictors support a deleterious effect. Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 13-32329496-A-G is Pathogenic according to our data. Variant chr13-32329496-A-G is described in ClinVar as Pathogenic/Likely_pathogenic. ClinVar VariationId is 52193.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000059.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRCA2	NM_000059.4	MANE Select	c.681+4A>G		splice_region intron	N/A	NP_000050.3	A0A7P0T9D7
	BRCA2	NM_001432077.1		c.681+4A>G		splice_region intron	N/A	NP_001419006.1	A0A7P0T9D7
	BRCA2	NM_001406720.1		c.681+4A>G		splice_region intron	N/A	NP_001393649.1	A0A8V8TPZ2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRCA2	ENST00000380152.8	TSL:5 MANE Select	c.681+4A>G		splice_region intron	N/A	ENSP00000369497.3	P51587
	BRCA2	ENST00000544455.6	TSL:1	c.681+4A>G		splice_region intron	N/A	ENSP00000439902.1	P51587
	BRCA2	ENST00000530893.7	TSL:1	c.312+4A>G		splice_region intron	N/A	ENSP00000499438.2	A0A590UJI7

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 27

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

ClinVar submissions

Significance: Pathogenic/Likely pathogenic

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
2	-	-	Hereditary breast ovarian cancer syndrome (2)
2	-	-	Hereditary cancer-predisposing syndrome (2)
1	-	-	Breast-ovarian cancer, familial, susceptibility to, 2 (1)
1	-	-	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Pathogenic	34
DANN	Benign	0.94
PhyloP100		2.6
Mutation Taster		=0/100	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.90
Splicevardb		3.0
SpliceAI score (max)		0.94		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.94		Position offset: 0
DS_DL_spliceai		0.62		Position offset: -4

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

Other links and lift over

dbSNP: rs397507884; hg19: chr13-32903633;