rs81002830

Positions:

• chr13-32319070-T-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BS1 BS2

The NM_000059.4(BRCA2):​c.68-7T>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0025 in 1,611,588 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★★).

• Frequency:
  • Genomes: 𝑓 0.0028 (1 hom., cov: 33)
  • Exomes 𝑓: 0.0025 (12 hom.)
• Consequence: BRCA2 NM_000059.4 splice_region, splice_polypyrimidine_tract, intron
• Scores: Splicing: ADA: 0.01713
• Clinical Significance: Benign reviewed by expert panel U:3 B:33
• Conservation: PhyloP100: 0.456

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 Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BP6: Variant 13-32319070-T-A is Benign according to our data. Variant chr13-32319070-T-A is described in ClinVar as [Benign]. Clinvar id is 52187.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32319070-T-A is described in Lovd as [Benign]. Variant chr13-32319070-T-A is described in Lovd as [Likely_benign].
• BS1: Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00281 (428/152318) while in subpopulation AMR AF= 0.00719 (110/15298). AF 95% confidence interval is 0.0061. There are 1 homozygotes in gnomad4. There are 251 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAdExome4 at 12 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRCA2	NM_000059.4	c.68-7T>A		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.68-7T>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		5	NM_000059.4	ENSP00000369497	A2

Frequencies

GnomAD3 genomes AF: 0.00282 AC: 429 AN: 152200 Hom.: 1 Cov.: 33

Gnomad AFR AF: 0.000458

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00720

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00290

Gnomad FIN AF: 0.00659

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00223

Gnomad OTH AF: 0.00430

GnomAD3 exomes AF: 0.00287 AC: 712 AN: 247874 Hom.: 3 AF XY: 0.00294 AC XY: 396 AN XY: 134568

Gnomad AFR exome AF: 0.000326

Gnomad AMR exome AF: 0.00259

Gnomad ASJ exome AF: 0.0134

Gnomad EAS exome AF: 0.000219

Gnomad SAS exome AF: 0.00190

Gnomad FIN exome AF: 0.00634

Gnomad NFE exome AF: 0.00242

Gnomad OTH exome AF: 0.00232

GnomAD4 exome AF: 0.00247 AC: 3603 AN: 1459270 Hom.: 12 Cov.: 32 AF XY: 0.00244 AC XY: 1768 AN XY: 725876

Gnomad4 AFR exome AF: 0.000930

Gnomad4 AMR exome AF: 0.00238

Gnomad4 ASJ exome AF: 0.0134

Gnomad4 EAS exome AF: 0.000101

Gnomad4 SAS exome AF: 0.00201

Gnomad4 FIN exome AF: 0.00581

Gnomad4 NFE exome AF: 0.00218

Gnomad4 OTH exome AF: 0.00335

GnomAD4 genome AF: 0.00281 AC: 428 AN: 152318 Hom.: 1 Cov.: 33 AF XY: 0.00337 AC XY: 251 AN XY: 74492

Gnomad4 AFR AF: 0.000457

Gnomad4 AMR AF: 0.00719

Gnomad4 ASJ AF: 0.0150

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00290

Gnomad4 FIN AF: 0.00659

Gnomad4 NFE AF: 0.00223

Gnomad4 OTH AF: 0.00426

Alfa AF: 0.00363 Hom.: 0

Bravo AF: 0.00229

EpiCase AF: 0.00311

EpiControl AF: 0.00296

ClinVar

Significance: Benign

Submissions summary: Uncertain:3 Benign:33

Revision: reviewed by expert panel

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 2 Uncertain:1 Benign:11

Benign, no assertion criteria provided	clinical testing	Sharing Clinical Reports Project (SCRP)	Apr 05, 2012	- -
Likely benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 27, 2017	This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Likely benign, criteria provided, single submitter	literature only	Counsyl	Jun 13, 2014	- -
Uncertain significance, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA2)	Dec 17, 2010	- -
Likely benign, criteria provided, single submitter	clinical testing	Pathway Genomics	Oct 30, 2014	- -
Benign, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Dec 30, 2015	- -
Likely benign, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -
Benign, criteria provided, single submitter	clinical testing	Michigan Medical Genetics Laboratories, University of Michigan	Nov 03, 2014	- -
Benign, no assertion criteria provided	clinical testing	BRCAlab, Lund University	Mar 02, 2020	- -
Likely benign, no assertion criteria provided	clinical testing	Department of Medical Genetics, University Hospital of North Norway	May 01, 2016	- -
Benign, criteria provided, single submitter	clinical testing	KCCC/NGS Laboratory, Kuwait Cancer Control Center	Jul 07, 2023	- -
Benign, reviewed by expert panel	curation	Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)	Apr 12, 2018	IARC class based on combined odds from multifactorial likelihood analysis, thresholds for class as per Easton et al. 2007 (PMID: 17924331). Class 1 Not Pathogenic based on posterior probability of pathogenicity = 7.44x10-115. There was no evidence for increased risk of breast cancer (OR 1.03; 95%CI 0.86-1.24) from case-control analysis of 83636 individuals. Nor for a deleterious effect of the variant when co-occurring with a pathogenic variant. Quantitative splicing analysis revealed an exon 3 exclusion rate of 13% in carriers compared to 3% in controls. Exon 3 exclusion from the variant allele is estimated at 20%. -

not specified Uncertain:1 Benign:5

Likely benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Oct 23, 2014	- -
Likely benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Mar 28, 2016	Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Multiple conflicting assertions about splice impact; ExAC: 0.5%(36/6594) Finnish chromosomes -
Uncertain significance, no assertion criteria provided	research	Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto	Jan 31, 2014	- -
Benign, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Aug 15, 2023	- -
Likely benign, criteria provided, single submitter	clinical testing	Cancer Genetics and Genomics Laboratory, British Columbia Cancer Agency	Apr 18, 2017	- -
Benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Nov 26, 2018	- -

Hereditary breast ovarian cancer syndrome Uncertain:1 Benign:4

Likely benign, criteria provided, single submitter	clinical testing	National Health Laboratory Service, Universitas Academic Hospital and University of the Free State	Nov 16, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Aug 23, 2016	Variant summary: The BRCA2 c.68-7T>A variant involves the alteration of a non-conserved intronic nucleotide. 2/5 splice prediction tools predict a significant impact on normal splicing. Although functional studies evaluating the splicing effect of this variant show a production of a exon 3 deletion transcript wild type control DNA also showed the production of this exon 3 deletion transcript albeit at a lesser quantitative amount (Sanz_2010 and Muller_2010). Furthermore, an additional functional study evaluating the variant of interest's effect on key aspects of BRCA2 function such homologous recombination and sensitivity to DNA damaging agents showed comparable abilities to the wild-type BRCA2. This variant was found in 282/118368 control chromosomes at a frequency of 0.0023824, which is approximately 3.2 times the estimated maximal expected allele frequency of a pathogenic BRCA2 variant (0.0007503), suggesting this variant is likely a benign polymorphism. This variant has been reported in many HBOC patients/families. It has been shown not to cosegregate with disease in two families (Santos_2014). In addition, the variant has been reported to co-occur with multiple different deleterious variants in BRCA1/2 (UMD), strongly suggesting for a benign outcome. Most of the clinical diagnostic laboratories in ClinVar have classified this variant as benign/likely benign. Taken together, this variant is classified as benign. -
Uncertain significance, flagged submission	clinical testing	Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia	Jul 21, 2015	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Likely benign, criteria provided, single submitter	clinical testing	Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C.	Jan 16, 2018	- -

Hereditary cancer-predisposing syndrome Benign:4

Benign, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Dec 05, 2014	- -
Benign, criteria provided, single submitter	clinical testing	Ambry Genetics	Nov 28, 2014	This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Benign, criteria provided, single submitter	curation	Sema4, Sema4	May 10, 2020	- -
Likely benign, no assertion criteria provided	clinical testing	True Health Diagnostics	Jun 27, 2017	- -

not provided Benign:3

Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Aug 21, 2023	- -
Benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Nov 01, 2024	BRCA2: BP4, BS1, BS2 -
Likely benign, no assertion criteria provided	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Dec 06, 2016	- -

Familial cancer of breast Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Apr 25, 2014	The variant is found in BRCA1-BRCA2,ENDOM-HEREDIC,BR-OV-HEREDIC panel(s). -
Likely benign, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Jan 01, 2019	- -

Breast and/or ovarian cancer Benign:1

Benign, criteria provided, single submitter

clinical testing

CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario

Apr 30, 2021

- -

Fanconi anemia complementation group D1 Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Apr 27, 2017

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -

BRCA2-related disorder Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Sep 26, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Malignant tumor of breast Benign:1

Benign, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

-

The c.68-7T>A variant has been identified in ~20 families (and 14 affected probands) from our laboratory with breast cancer and 82 times in the UMD-BRCA2 database. In the literature, the variant was identified in 12 of 5594 proband chromosomes from individuals with breast and ovarian cancer, although an inadequate number of control chromosomes were tested to establish the variants' frequency in the general population such that the full spectrum of benign variation may not yet been defined for this gene, and increasing the possibility that this may be a benign variant (Hilton 2002, Muller 2011, Santarosa 1999, Thirthagiri 2008). The variant was identified by the ESP project (0.0015 in EU; 0.0002 in AA), and was identified in the Exome Aggregation Consortium (ExAC) database in all populations listed (European (Non-Finnish), East Asian, African, Latino, South Asian, European (Finnish)) with an overall frequency of 0.002, suggesting this may be a low frequency variant. In addition, this variant was identified by our laboratory in one individual who was homozygous for this variant who developed bilateral breast cancer late in life and the variant was suspected to segregate (in heterozygous form) with breast cancer in two other individuals in the family. However, homozygous deleterious variants of the BRCA2 gene have been demonstrated to cause Fanconi-Anemia, which was not reported in this individual, and increasing the likelihood that this variant is benign, but this information does not rule out the possibility that this variant could have contributed to the cancer in this family. The variant is listed in dbSNP database as coming from a "clinical source" (ID#: rs81002830) and had a frequency of 0.002 in the 1000 Genomes project. This variant was identified in ClinVar (by Invitae as Likely Benign, GeneDx as Benign, Sharing clinical reports project derived from Myriad reports as Uncertain significance (as of 2012 - more recently, in a personal communication Myriad has re-classified this variant as a polymorphism), by the BIC database as Uncertain significance. The c.68-7T>A variant is located in the 3' splice region but does not affect the invariant -1 and -2 positions. However, positions -3 and -5 to -12 are part of the splicing consensus sequence and variants involving these positions sometimes affect splicing. In-silico or computational prediction software (SpliceSiteFinder, MaxEntScan, NNSPLICE, HumanSpliceFinder) predicts a greater than 10% difference in splicing in 2 of 4 different programs. However, this information is not predictive enough to rule in or out pathogenicity. Studies have shown the increased rate of exon 3 skipping for this variant (20-30%), but this has also been observed in controls (Muller 2011, Thery 2011, Sanz 2010, Vreeswijk 2009, Houdayer 2012, Santorosa 1999). The c.68-7T>A variant and two other variants located at the same nucleotide position (c.68-7delT, and one c.68-78delAA) were all found to sometimes co-occur with a pathogenic BRCA2 mutation (Muller 2011), increasing the likelihood that this variant does not have clinical significance. In the UMD database, the variant was identified as co-occurring with another pathogenic variant 9x (4x in BRCA2 with: c.1796_1800delCTTAT (p.Ser599X) or c.5130_5133delTGTA (p.Tyr1710X)). In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as benign. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	5.6
DANN	Benign	0.65

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.017
dbscSNV1_RF	Benign	0.10
SpliceAI score (max)		0.050		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs81002830; hg19: chr13-32893207; COSMIC: COSV66457916; COSMIC: COSV66457916;