chr13-32370556-A-G

Position:

• chr13-32370556-A-G

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM2 PM5 PP5_Very_Strong

The NM_000059.4(BRCA2):​c.8486A>G​(p.Gln2829Arg) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000000687 in 1,456,384 control chromosomes in the GnomAD database, with no homozygous occurrence. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q2829H) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: BRCA2 NM_000059.4 missense, splice_region
• Scores: Splicing: ADA: 0.9956
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:12 U:1
• Conservation: PhyloP100: 5.99

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 12 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr13-32370557-G-T is described in Lovd as [Likely_pathogenic].
• PP5: Variant 13-32370556-A-G is Pathogenic according to our data. Variant chr13-32370556-A-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 38161.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-32370556-A-G is described in Lovd as [Pathogenic]. Variant chr13-32370556-A-G is described in Lovd as [Pathogenic]. Variant chr13-32370556-A-G is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRCA2	NM_000059.4	c.8486A>G	p.Gln2829Arg	missense_variant, splice_region_variant	19/27	ENST00000380152.8	NP_000050.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BRCA2	ENST00000380152.8	c.8486A>G	p.Gln2829Arg	missense_variant, splice_region_variant	19/27	5	NM_000059.4	ENSP00000369497	A2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.87e-7 AC: 1 AN: 1456384 Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1 AN XY: 724932

Gnomad4 AFR exome AF: 0.00

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: 9.03e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

EpiCase AF: 0.00

EpiControl AF: 0.0000593

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:12 Uncertain:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 2 Pathogenic:3 Uncertain:1

Pathogenic, criteria provided, single submitter	clinical testing	Genetics and Molecular Pathology, SA Pathology	Apr 20, 2021	The BRCA2:c.8486A>G variant is classified as PATHOGENIC (PVS1_O_Strong, PM2, PP3, PP1_Strong). BRCA2:c.8486A>G is a single nucleotide substitution in exon 19 that predicts a missense change from Glutamine to Arginine at position 2829; NP_000050.2(BRCA2).p.(Gln2829Arg). This variant resides at the penultimate coding nucleotide upstream of the adjacent splice donor boundary. No alternative wildtype splice isoforms exist for this gene. BRCA2:c.8486A>G (rs80359100) is not recorded in gnomAD nor the control database FLOSSIES (PM2). Computational analysis supports a deleterious effect, predicting loss of normal wildtype splicing at the adjacent intron19 splice donor site (Alamut Visual Plus 1.5.1) (PP3). Independent splicing assays confirm this variant disrupts normal mRNA splicing, causing in-frame skipping of exon 19 resulting in a transcript that encodes loss of 51 amino acids from the highly conserved DNA binding domain important to normal BRCA2 function (Houdayer et al., 2012 PMID:22505045, Acedo et al., 2015 PMID:25382762, Kraus et., 2017 PMID:27616075, Wai et al., 2020 PMID:32123317) (PVS1_O_Strong). Another BRCA2 splicing variant (BRCA2:c.8487+1G>A) downstream of BRCA2:c.8486A>G also causes in-frame skipping of exon 19 and has been classified as pathogenic by the ENIGMA Expert Panel (ClinVar Variation ID: 52602). BRCA2:c.8486A>G has been reported in the scientific literature in multiple unrelated individuals with breast cancer (Kraus et al., 2017 PMID:27616075, Lee et al., 2018 PMID:30415210). This variant demonstrates disease segregation in 2 unrelated families with BRCA2-related cancers (South Australian Clinical Genetics Service; personal communication) (PP1_Strong). Multiple diagnostic laboratories report this variant as Pathogenic/Likely Pathogenic in patients with hereditary breast and ovarian cancer syndrome (ClinVar Variation ID: 38161). This variant is listed in HGMD as ‘disease causing mutation?’ in association with Breast cancer (Accession: CM128970). -
Likely pathogenic, no assertion criteria provided	clinical testing	Institute of Human Genetics, Medical University Innsbruck	Feb 11, 2015	- -
Uncertain significance, flagged submission	clinical testing	Sharing Clinical Reports Project (SCRP)	May 01, 2012	- -
Pathogenic, criteria provided, single submitter	clinical testing	Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge	Oct 02, 2015	- -

Breast and/or ovarian cancer Pathogenic:2

Pathogenic, no assertion criteria provided	clinical testing	CZECANCA consortium	Jun 11, 2019	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	May 01, 2023	- -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	May 14, 2024	The BRCA2 c.8486A>G (p.Gln2829Arg) variant has been reported in the published literature in individuals and families with breast and/or ovarian cancer (PMIDs: 33875706 (2021), 29446198 (2018), 27616075 (2016), 22762150 (2012), 12601471 (2003)). Experimental studies show the variant is damaging to protein function by reducing cell survival (PMID: 33293522 (2020)) and causing improper splicing of exon 19 (PMIDs: 34663891 (2021), 32123317 (2020), 27060066 (2016), 22505045 (2012), 16489001 (2006)). A multifactorial likelihood analysis reports a posterior probability suggestive of the variant being pathogenic (PMID: 31131967 (2019)). This variant has not been reported in large, multi-ethnic general populations (Genome Aggregation Database, http://gnomad.broadinstitute.org). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, this variant is classified as pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	Jun 12, 2023	PM4, PM2_SUP, PS3, BP4 -

Hereditary cancer-predisposing syndrome Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Apr 18, 2023	This variant changes the penultimate nucleotide c.A of exon 19 of the BRCA2 gene and is predicted to impair RNA splicing at the intron 19 splice donor site. This variant is also known as 8714A>G in the literature. RNA studies using carrier-derived lymphocytes have shown that this variant causes in-frame skipping of exon 19 (PMID: 22505045, 29750258, 32123317). A functional study has reported this variant impacts BRCA2 function in the rescue of Brca2-deficient mouse embryonic stem cells (PMID: 33293522). This variant has been reported in individuals affected with breast or ovarian cancer, including a male individual (PMID: 23146383, 27616075, 33875706). This variant has been observed in at least 4 suspected hereditary breast and ovarian cancer families (PMID: 16489001, 20815029, 26014432, 29446198, 31409081). A multifactorial analysis reported this variant to have a segregation likelihood ratio for pathogenicity of 14.295, derived from 3 families (PMID: 31131967). 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	clinical testing	Ambry Genetics	Sep 13, 2022	The p.Q2829R variant (also known as c.8486A>G) is located in coding exon 18 of the BRCA2 gene. This results from an A to G substitution at nucleotide position 8486 which is the second to last nucleotide of the exon. The glutamine at codon 2829 is replaced by arginine, an amino acid with highly similar properties. This alteration has been identified in multiple breast cancer cohorts, including male breast cancer (Scott CL et al. Hum Genet, 2003 May;112:542-51; Deb S et al. BMC Cancer, 2012 Nov;12:510; Kim JH et al. Sci Rep, 2021 04;11:8485). Multiple RNA studies have shown that this alteration, as well as a close match alteration BRCA2 c.8486A>T, leads to skipping of coding exon 18 (Houdayer C et al. Hum Mutat. 2012 Aug;33(8):1228-38; Kraus C et al. Int. J. Cancer. 2017 Jan;140:95-102; Acedo A et al. Hum. Mutat. 2015 Feb;36:210-21; Machackova E et al. Klin Onkol. 2019;32:51-71; Wai HA et al. Genet Med, 2020 06;22:1005-1014; Biswas K et al. NPJ Genom Med, 2020 Dec;5:52). Of note, this alteration is also referred to as 8714A>G in the published literature. This amino acid and nucleotide position is well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by protein in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

Hereditary breast ovarian cancer syndrome Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Feb 07, 2017	Variant summary: The BRCA2 c.8486A>G (p.Gln2829Arg) variant involves the alteration of a conserved nucleotide, which 4/5 in silico tools predict a damaging outcome for this variant. This variant is located at < 2nt from the intron-exon junction, which 3/5 splice prediction tools predict a significant impact on normal splicing and ESE finder predicting that this variant may affect ESE binding sites for SRp50 and SF2/ASF and might add binding sites for SRp55. One functional study, Houdayer _2012, testing this variant in lymphocytes found it to cause an inframe mutation resulting in exon 19 skipping, with no wildtype transcript being produced. This variant is absent in 120974 control chromosomes, which does not exceed the estimated maximum expected allele frequency for a pathogenic BRCA2 variant of 1/1333. The variant was observed in affected individuals via publications. Multiple clinical diagnostic laboratories/reputable databases have reported the variant with conflicting classifications, predominantly as "likely pathogenic/pathogenic," and others classifying it as "uncertain significance." Taken together, this variant is classified as likely pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Sep 01, 2022	This missense change has been observed in individual(s) with several individuals with a personal or family history of breast cancer and a personal or family history of breast cancer (PMID: 22505045, 22762150, 27616075, 29446198, 30415210). For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the BRCA2 protein in which other variant(s) (p.Gly2793Arg) have been determined to be pathogenic (PMID: 12442275, 15889636, 16030099, 23108138, 23233716, 25777348). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. Studies have shown that this missense change results in skipping of exon 19, but is expected to preserve the integrity of the reading-frame (PMID: 16489001, 22505045, 27616075). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 38161). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glutamine, which is neutral and polar, with arginine, which is basic and polar, at codon 2829 of the BRCA2 protein (p.Gln2829Arg). RNA analysis indicates that this missense change induces altered splicing and likely results in a shortened protein product. -

BRCA2-related cancer predisposition Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

All of Us Research Program, National Institutes of Health

Mar 25, 2024

This variant changes the penultimate nucleotide c.A of exon 19 of the BRCA2 gene and is predicted to impair RNA splicing at the intron 19 splice donor site. This variant is also known as 8714A>G in the literature. RNA studies using carrier-derived lymphocytes have shown that this variant causes in-frame skipping of exon 19 (PMID: 22505045, 29750258, 32123317). A functional study has reported this variant impacts BRCA2 function in the rescue of Brca2-deficient mouse embryonic stem cells (PMID: 33293522). This variant has been reported in individuals affected with breast or ovarian cancer, including a male individual (PMID: 23146383, 27616075, 33875706). This variant has been observed in at least 4 suspected hereditary breast and ovarian cancer families (PMID: 16489001, 20815029, 26014432, 29446198, 31409081). A multifactorial analysis reported this variant to have a segregation likelihood ratio for pathogenicity of 14.295, derived from 3 families (PMID: 31131967). Loss of BRCA2 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Likely Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.25
BayesDel_addAF	Pathogenic	0.19	D
BayesDel_noAF	Uncertain	0.040
CADD	Pathogenic	27
DANN	Uncertain	1.0
Eigen	Uncertain	0.64
Eigen_PC	Uncertain	0.61
FATHMM_MKL	Pathogenic	0.97	D
M_CAP	Uncertain	0.18	D
MetaRNN	Uncertain	0.72	D;D
MetaSVM	Uncertain	-0.040	T
MutationTaster	Benign	1.0	D;D
PrimateAI	Uncertain	0.54	T
PROVEAN	Benign	-1.1	N;N
REVEL	Uncertain	0.42
Sift	Pathogenic	0.0	D;D
Sift4G	Uncertain	0.015	D;D
Vest4		0.62
MutPred		0.36		Gain of MoRF binding (P = 0.018);Gain of MoRF binding (P = 0.018);
MVP		0.93
MPC		0.17
ClinPred		0.99	D
GERP RS		5.2
gMVP		0.76

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.98
SpliceAI score (max)		0.36		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.36		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: rs80359100; hg19: chr13-32944693;