13-32325184-G-A

Variant names:

• chr13-32325184-G-A
• rs397507713
• NM_000059.4:c.425G>A

Variant summary

Our verdict is Likely pathogenic. The variant received 7 ACMG points: 7P and 0B. PM5 PP3_Strong PP5

The NM_000059.4(BRCA2):​c.425G>A​(p.Ser142Asn) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0000285 in 1,544,990 control chromosomes in the GnomAD database, including 1 homozygotes. 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S142I) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000031 (1 hom.)
• Consequence: BRCA2 NM_000059.4 missense, splice_region
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:5 U:4
• Conservation: PhyloP100: 4.91
• Publications: 21 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):

• breast-ovarian cancer, familial, susceptibility to, 2

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

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, ClinGen, G2P
• 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: Likely_pathogenic. The variant received 7 ACMG points.

• PM5: Other missense variant is known to change same aminoacid residue: Variant chr13-32325184-G-T is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 51618.
• 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 13-32325184-G-A is Pathogenic according to our data. Variant chr13-32325184-G-A is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 197099.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRCA2	NM_000059.4	c.425G>A	p.Ser142Asn	missense_variant, splice_region_variant	Exon 4 of 27	ENST00000380152.8	NP_000050.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRCA2	ENST00000380152.8	c.425G>A	p.Ser142Asn	missense_variant, splice_region_variant	Exon 4 of 27	5	NM_000059.4	ENSP00000369497.3
BRCA2	ENST00000530893.7	c.56G>A	p.Ser19Asn	missense_variant, splice_region_variant	Exon 4 of 27	1		ENSP00000499438.2
BRCA2	ENST00000614259.2	n.425G>A		splice_region_variant, non_coding_transcript_exon_variant	Exon 3 of 26	2		ENSP00000506251.1

Frequencies

GnomAD3 genomes AF: 0.00000658 AC: 1 AN: 152036 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000322 AC: 8 AN: 248562 AF XY: 0.0000520

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000309 AC: 43 AN: 1392954 Hom.: 1 Cov.: 26 AF XY: 0.0000460 AC XY: 32 AN XY: 696402

African (AFR) AF: 0.00 AC: 0 AN: 31826

American (AMR) AF: 0.00 AC: 0 AN: 44600

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25728

East Asian (EAS) AF: 0.00 AC: 0 AN: 39262

South Asian (SAS) AF: 0.000355 AC: 30 AN: 84620

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52642

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5572

European-Non Finnish (NFE) AF: 0.0000124 AC: 13 AN: 1050542

Other (OTH) AF: 0.00 AC: 0 AN: 58162

GnomAD4 genome AF: 0.00000658 AC: 1 AN: 152036 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 74248

African (AFR) AF: 0.00 AC: 0 AN: 41386

American (AMR) AF: 0.00 AC: 0 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.00 AC: 0 AN: 4818

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10592

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.0000147 AC: 1 AN: 68002

Other (OTH) AF: 0.00 AC: 0 AN: 2090

Alfa AF: 0.0000285 Hom.: 0

Bravo AF: 0.00000756

ExAC AF: 0.0000412 AC: 5

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:5 Uncertain:4

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:2 Uncertain:1

Feb 17, 2016

Eurofins Ntd Llc (ga)

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Jun 19, 2019

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The best available variant frequency is uninformative because it is below the disease allele frequency. Found in at least one symptomatic patient. Predicted to have a damaging effect on the protein. One other pathogenic or likely pathogenic variant affects the same amino acid. Predicted to negatively affect a known splice site.

Aug 28, 2024

GeneDx

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

A different exonic splice variant at this same splice site, c.425G>T, results in the production of multiple transcripts, including potentially functional in-frame transcripts (PMID: 21638052, 32398771, 33469799); In silico analysis indicates that this missense variant does not alter protein structure/function; Also known as 653G>A; This variant is associated with the following publications: (PMID: 21638052, 29446198, 31131967, 32782288, 33469799, 32398771, 32853339, 33471991, 29922827)

Hereditary breast ovarian cancer syndrome Pathogenic:2

Oct 08, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces serine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 142 of the BRCA2 protein (p.Ser142Asn). RNA analysis indicates that this missense change induces altered splicing and may result in an absent or altered protein product. This variant is present in population databases (rs397507713, gnomAD 0.03%). This missense change has been observed in individual(s) with breast and/or ovarian cancer, prostate cancer (PMID: 21638052, 29446198, 32853339). ClinVar contains an entry for this variant (Variation ID: 197099). Based on a multifactorial likelihood algorithm using genetic, in silico, and/or statistical data, this variant has been determined to have a low probability of being pathogenic (PMID: 31131967). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this missense change results in skipping of exon 4, and produces a non-functional protein and/or introduces a premature termination codon (internal data). This variant disrupts the c.425G nucleotide in the BRCA2 gene. Other variant(s) that disrupt this nucleotide have been determined to be pathogenic (PMID: 21638052, 31131967). This suggests that this nucleotide is clinically significant, and that variants that disrupt this position are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

Nov 16, 2024

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: BRCA2 c.425G>A (p.Ser142Asn) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. As the variant alters the last conserved nucleotide of exon 4 adjacent to the canonical splice donor site, several computational tools predict a significant impact on normal splicing: Two predict the variant weakens the canonical 5' splicing donor site. Two predict the variant abolishes the canonical 5' splicing donor site. Studies have shown that this missense change affects mRNA splicing by skipping of exon 4 and introduces a premature termination codon (Internal data). The variant allele was found at a frequency of 3.2e-05 in 248562 control chromosomes. c.425G>A has been reported in the literature in settings of multigene panel testing in individuals affected with breast, renal, colorectal, or prostate cancers (examples: Feliubadalo_2019, Kemp_2019, Hartman_2020, Rebbeck_2018, Darst_2021). These data indicate that the variant is likely to be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 32853339, 30927264, 32782288, 31125106, 29446198, Internal Data). ClinVar contains an entry for this variant (Variation ID: 197099). Based on the evidence outlined above, the variant was classified as likely pathogenic.

Hereditary cancer-predisposing syndrome Uncertain:2

Nov 05, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.425G>A variant (also known as p.S142N), located in coding exon 3 of the BRCA2 gene, results from a G to A substitution at nucleotide position 425. The serine at codon 142 is replaced by asparagine, an amino acid with highly similar properties. However, this change occurs in the last base pair of coding exon 3, which makes it likely to have effect on normal mRNA splicing. Based on data from gnomAD, the frequency for this variant is above the maximum credible frequency for a disease-causing variant in this gene based on internally established thresholds (Karczewski et al. Nature. 2020 May;581(7809):434-443; Whiffin et al. Genet Med. 2017 10;19:1151-1158). However, in silico splice site analysis predicts that this alteration will weaken the native splice donor site; and RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). Another variant at this position, BRCA2 c.425G>T, which has a similar splicing profile to this alteration, was able to rescue the growth defect in BRCA2-null mouse embryonic stem cells and those surviving cells maintained partial activity in a homology directed DNA repair functional assay (Mesman R et al. Genet Med 2020 Aug;22(8):1355-1365). BRCA2 c.425G>T was also identified in patients who collectively have a phenotype that is not consistent with a high risk BRCA2 pathogenic variant (Nix P et al. Fam Cancer, 2021 Jan). Since supporting evidence is conflicting at this time, the clinical significance of this alteration remains unclear.

Jun 14, 2023

Color Diagnostics, LLC DBA Color Health

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This missense variant replaces serine with asparagine at codon 142 of the BRCA2 protein. This variant alters the conserved c.G at the last nucleotide position of exon 4 to c.A. Splice prediction tools suggest that this variant is likely to disrupt RNA splicing. A different nucleotide change occurring at the same position c.425G>T is known to disrupt splicing of exon 4 (PMID: 21638052). However, the c.425G>T variant is reported to also produce some transcripts lacking exon 4 and downstream exon(s) that may retain some function (PMID: 32398771, 33469799). Functional and RNA studies have not been reported for this c.425G>A variant. This variant has been reported in an individual affected with breast and renal cancer (PMID: 32782288), an individual affected with prostate cancer (PMID: 32853339) and in a breast cancer case-control meta-analysis in 1/60466 cases and 1/53461 unaffected individuals (PMID: 33471991; Leiden Open Variation Database DB-ID BRCA2_003686). A multifactorial analysis has reported likelihood ratios for pathogenicity based on segregation and tumor pathology of 1.5539 and 0.89, respectively (PMID: 31131967). This variant has been identified in 8/248562 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

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

Oct 02, 2015

Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Familial cancer of breast Uncertain:1

Oct 03, 2023

Baylor Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.45
BayesDel_addAF	Benign	-0.26	T
BayesDel_noAF	Benign	-0.31
CADD	Pathogenic	33
DANN	Uncertain	1.0
DEOGEN2	Benign	0.0	.;.
Eigen	Pathogenic	0.75
Eigen_PC	Pathogenic	0.75
LIST_S2	Benign	0.0	.;.
M_CAP	Uncertain	0.25	D
MetaRNN	Benign	0.29	T;T
MetaSVM	Benign	-1.2	T
MutationAssessor	Benign	0.0	.;.
PhyloP100		4.9
PrimateAI	Benign	0.43	T
PROVEAN	Benign	-0.76	N;N
Sift	Pathogenic	0.0	D;D
Sift4G	Pathogenic	0.0	D;D
Vest4		0.37
ClinPred		0.46	T
GERP RS		5.8
gMVP		0.49
Mutation Taster		=2/98	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	1.0
SpliceAI score (max)		0.91		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.91		Position offset: 0

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

Other links and lift over

dbSNP: rs397507713; hg19: chr13-32899321;