13-32362596-A-T

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1 PM2 PM5 PP3_Moderate PP5_Very_Strong

The NM_000059.4(BRCA2):c.7879A>T(p.Ile2627Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,850 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I2627V) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000027 (0 hom.)
• Consequence: BRCA2 NM_000059.4 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:24 U:1 B:1
• Conservation: PhyloP100: 3.53

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 16 ACMG points.

• PM1: In a hotspot region, there are 6 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 4 benign, 16 uncertain in NM_000059.4
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr13-32362597-T-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 230735.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.921
• PP5: Variant 13-32362596-A-T is Pathogenic according to our data. Variant chr13-32362596-A-T is described in ClinVar as [Pathogenic]. Clinvar id is 52430.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr13-32362596-A-T is described in Lovd as [Pathogenic]. Variant chr13-32362596-A-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRCA2	NM_000059.4	c.7879A>T	p.Ile2627Phe	missense_variant	17/27	ENST00000380152.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRCA2	ENST00000380152.8	c.7879A>T	p.Ile2627Phe	missense_variant	17/27	5	NM_000059.4	A2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000274 AC: 4 AN: 1461850 Hom.: 0 Cov.: 33 AF XY: 0.00000550 AC XY: 4 AN XY: 727226

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: 0.00000360

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:24 Uncertain:1 Benign:1

Revision: reviewed by expert panel

Submissions by phenotype

not provided Pathogenic:9

Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Sep 01, 2020	- -
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	-	The p.Ile2627Phe variant was identified in 1 of 4206 proband chromosomes (frequency: 0.0001) from individuals or families with bilateral and unilateral breast cancer (Borg 2010); however, control chromosomes were not evaluated in these studies, thus the prevalence of this variant in the general population could not be determined. The variant was identified in dbSNP (ID: rs80359014) “With Pathogenic, Uncertain significance allele.” The p.Ile2627Phe variant was also identified in GeneInsight COGR database by 2 submitters, one classified as pathogenic and the other as VUS. In Clinvar database, the variant was identified and classified as pathogenic by ENIGMA and by the Sharing Clinical Reports Project, derived from Myriad reports; it was classified as likely pathogenic by Ambry Genetics and no classification was provided by Invitae. The BRCA Share UMD Database identified the variant 1x and classified it as causal and ARUP Laboratories identified the variant 1x and classified it definitely pathogenic. In BIC database the variant was identified 7x with unknown clinical significance. The variant was not identified in NHLBI Exome Sequencing Project (Exome Variant Server) and Exome Aggregation Consortium (ExAC), COSMIC, Clinvitae or MutDB. The p.Ile2627 residue is conserved across mammals and lower organisms, and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the Phenylalanine (Phe) variant may impact the protein. However, this information is not predictive enough to assume pathogenicity. In addition, Multifactorial likelihood-ratio modelling, homology-directed repair assay and centrosome percent amplification assay, suggest that the variant disrupts BRCA2 function (Farrugia 2008, Easton 2007). Studies on protein likelihood ratio modelling is in favour of protein loss of function (Karchin 2008) and based on multifactorial probability-based model for assessing pathogenicity, the prior probability of being deleterious is 0.29 and posterior probability of being deleterious 1.00 (Lindor 2012).In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Jun 05, 2019	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	Nov 03, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jun 06, 2022	Published functional studies demonstrate a damaging effect: reduced homology directed repair activity and an increase in centriole amplification when compared to wild-type (Farrugia 2008, Guidugli 2013, Guidugli 2018); Multifactorial studies suggest this variant is associated with breast and ovarian cancer (Lindor 2012); Observed in individuals with BRCA2-related cancers (Spitzer 2000, Balabas 2010, Stegel 2011, Lee 2014, Meisel 2017, Jakimovska 2018); In silico analysis supports that this missense variant does not alter protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); Also known as 8107A>T; This variant is associated with the following publications: (PMID: 29368341, 29394989, 25447315, 22430266, 19043619, 21232165, 25452441, 21520273, 24323938, 25146914, 17924331, 21990134, 25948282, 20104584, 20383589, 26295337, 18451181, 23108138, 10699917, 28324225, 29335924, 29884841, 33964450, 30787465, 29988080, 29446198, 32444794, 12228710) -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Mar 26, 2021	In the published literature, the variant has been reported in individuals and families with breast cancer (PMID: 29335924 (2018), 25948282 (2015), 25452441 (2015), 21232165 (2011), 20104584 (2010), 18451181 (2008)), and it has been classified as pathogenic in multifactorial analysis studies (PMID: 17924331 (2007), 21990134 (2012)). Additional functional studies indicate the variant has deleterious effects on BRCA2 protein functions (PMID: 23108138 (2013), 29988080 (2018)). Based on the available information, this variant is classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	GeneKor MSA	Jan 01, 2020	This variant results in the substitution of Isoleucine to Phenylalanine at amino acid residue 2627 of the BRCA2 protein. The Isoleucine residue is highly conserved among species and is located in a functional domain of the protein and there is a small physiochemical difference between Isoleucine and Phenylalanine (Grantham Score 21). This variant has been reported in the literature in patients and families with breast and/or ovarian cancer (PMID: 10699917, 20104584, 25452441). Also, this variant has been described as 8107A>T in the literature and is absent in population databases (rs80359014). The mutation database ClinVar contains entries for this variant (Variation ID: 52430). Algorithms developed to predict the effect of missense changes on protein structure and function suggest that this variant may be damaging to the protein and this prediction has also been observed experimentally. Experimental studies have shown that this variant affects BRCA2 homology-directed repair activity while loss of the protein function results in cell death (PMID: 18451181, 23108138, 25146914). -
Pathogenic, criteria provided, single submitter	clinical testing	Human Genetics Bochum, Ruhr University Bochum	Jan 04, 2022	ACMG criteria used to clasify this variant: PP3, PS3, PM1, PS4, PM2 -

Breast-ovarian cancer, familial, susceptibility to, 2 Pathogenic:6 Uncertain:1

Uncertain significance, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA2)	Feb 20, 2004	- -
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	Aug 26, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Feb 07, 2023	_x000D_ Criteria applied: PS3, PS4, PM2_SUP, PP3 -
Pathogenic, reviewed by expert panel	curation	ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen	Apr 23, 2024	The c.7879A>T variant in BRCA2 is a missense variant predicted to cause substitution of Isoleucine by Phenylalanine at amino acid 2627 (p.Ile2627Phe). This variant is absent from gnomAD v2.1 (exomes only, non-cancer subset, read depth >=25) and gnomAD v3.1 (non-cancer subset, read depth >=25) (PM2_Supporting met). This BRCA2 missense variant is within a key functional domain and the computational predictor BayesDel (noAF) gives a score of 0.25 indicating that impact on BRCA2 function via protein change is unclear (score range 0.18-0.30). SpliceAI predictor score of 0.00 suggests that the variant has no impact on splicing (score threshold <0.10) (no bioinformatic code is applied). Reported by three calibrated studies to exhibit protein function similar to pathogenic control variants (PMIDs: 29988080, 33609447, 32444794) (PS3 met). Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 406 (based on Cosegregation LR=1.88; Co-occurrence LR=1.28; Family History LR=168.6), above the threshold for Very strong evidence towards pathogenicity (LR >350) (PP4_Very strong met; PMID: 17924331, 31853058). In summary, this variant meets the criteria to be classified as a Pathogenic variant for BRCA2-related cancer predisposition based on the ACMG/AMP criteria applied as specified by the ENIGMA BRCA1/2 VCEP (PM2_Supporting, PP4_Very strong, PS3). -
Pathogenic, criteria provided, single submitter	clinical testing	Michigan Medical Genetics Laboratories, University of Michigan	Apr 21, 2016	- -
Pathogenic, no assertion criteria provided	clinical testing	Sharing Clinical Reports Project (SCRP)	Mar 11, 2012	- -

Familial cancer of breast Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Jul 18, 2023	Criteria applied: PS3,PS4,PM2_SUP,PP3 -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Dec 02, 2022	- -
Pathogenic, no assertion criteria provided	research	Department of Medical Laboratory Science, Faculty of Allied Health Sciences, University of Peradeniya	Oct 19, 2019	- -

Hereditary breast ovarian cancer syndrome Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Feb 21, 2020	Variant summary: BRCA2 c.7879A>T (p.Ile2627Phe) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251356 control chromosomes. c.7879A>T has been well reported in the literature in multiple individuals affected with Hereditary Breast and Ovarian Cancer in literature spanning over ten years to include multifactorial probability models for assessing pathogenic outcomes (example, Borg_2010, Capanu_2011, Stegel_2011, Spitzer_2000, Kluska_2015, Couch_2015, Rebbeck_2018, Lindor_2012, Easton_2007). These data indicate that the variant is very likely to be associated with disease. At-least one co-occurrence with another pathogenic variant has been reported in a patient with triple negative breast cancer (PALB2 c.2470dupT, p.Cys824LeufsX2)(Couch_2015). However, this does not rule out the pathogenicity of this variant due to the possibility of mutual exclusivity of the two variants. Several publications report experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in an inability to complement the lethality of mBRCA2-deficient mouse-embryonic stem (mES) cells (example, Hendriks_2014 and Mesman_2019) as well as decreased homology directed repair activity (example, Farrugia_2008, Guidguli_2012). One expert panel (ENIGMA) and ten clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Some submitters cite overlapping evidence utilized in the context of this evaluation. All submitters classified the variant as pathogenic (n=8)/likely pathogenic (n=3). Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Nov 28, 2023	This sequence change replaces isoleucine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 2627 of the BRCA2 protein (p.Ile2627Phe). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with breast and/or ovarian cancer and prostate cancer (PMID: 10699917, 20104584, 20383589, 21232165, 25452441, 29335924, 29368341). This variant is also known as 8107A>T. ClinVar contains an entry for this variant (Variation ID: 52430). Advanced modeling performed at Invitae incorporating data from internal and/or published experimental studies (PMID: 33609447) indicates that this missense variant is expected to disrupt BRCA2 function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects BRCA2 function (PMID: 18451181, 23108138, 25146914, 29394989, 29884841). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, no assertion criteria provided	research	Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto	Jan 31, 2014	- -

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Dec 05, 2023	This missense variant replaces isoleucine with phenylalanine at codon 2627 in the DNA binding domain of the BRCA2 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). Functional studies have reported that this variant impacts BRCA2 function in homology-mediated repair and complementation of Brca2-deficient mouse embryonic stem cells (PMID: 18451181, 23108138, 29394989, 29988080, 33609447). This variant has been reported in over ten individuals affected with breast cancer (PMID: 10699917, 20104584, 20383589, 21520273, 29335924) and prostate cancer (PMID: 29368341). This variant also has been reported with a family history likelihood ratio for pathogenicity of 2.61 (PMID: 18451181), and it has been observed in six breast cancer-affected individuals of Macedonian origin, who showed significant family history of BRCA2-related cancers (PMID: 29335924). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Dec 13, 2023	The p.I2627F variant (also known as c.7879A>T), located in coding exon 16 of the BRCA2 gene, results from an A to T substitution at nucleotide position 7879. The isoleucine at codon 2627 is replaced by phenylalanine, an amino acid with highly similar properties. This alteration has been classified as pathogenic (p>0.99) by multifactorial analysis, which integrates the following lines of evidence to produce a quantitative likelihood of pathogenicity: in silico prediction models, segregation with disease, tumor characteristics, mutation co-occurrence, and functional assay results (Easton D et al. Am J Hum Genet. 2007;81:873-883; Vallee M et al. Hum Mutat. 2012 Jan;33(1):22-8; Lindor NM et al. Hum. Mutat. 2012;33(1):8-21; Hendriks G et al. Hum. Mutat. 2014;35(11):1382-91). In multiple studies, this alteration was detected in several individuals with breast or ovarian cancer (Spitzer E et al. Int. J. Cancer 2000;85(4):474-81; Balabas A et al. Fam. Cancer 2010;9(3):267-74; Stegel V et al. BMC Med. Genet. 2011;12():9; Kluska A et al. BMC Med Genomics 2015;8():19; Couch FJ et al. J. Clin. Oncol. 2015;33(4):304-11; Meisel C et al. Arch. Gynecol. Obstet. 2017 May;295(5):1227-1238; Zakrzewski F et al. BMC Cancer 2019 Apr;19(1):396). This alteration was identified in 1/150 unselected patients with recurrent or metastatic prostate cancer (Isaacsson Velho P et al. Prostate 2018 04;78:401-407). A homology-directed DNA repair (HDR) assay demonstrated p.I2627F to have low functionality, with a probability of pathogenicity of 0.990 (Guidugli L et al. Am. J. Hum. Genet. 2018 Feb;102(2):233-248). In another study, this variant was non-functional in a homology-directed DNA repair (HDR) assay (Hart SN et al. Genet Med. 2019 01;21:71-80). In addition, a mouse embryonic stem cell assay showed that p.I2627F was unable to complement Brca2-deficient cell lethal phenotype (Mesman R et al. Genet. Med. 2019 02;21(2):293-302). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

Medulloblastoma;C0346153:Familial cancer of breast;C0376358:Malignant tumor of prostate;C1838457:Fanconi anemia complementation group D1;C2675520:Breast-ovarian cancer, familial, susceptibility to, 2;C2751641:Glioma susceptibility 3;C3150546:Pancreatic cancer, susceptibility to, 2;CN033288:Wilms tumor 1 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Oct 31, 2018

- -

not specified Benign:1

Benign, no assertion criteria provided

research

King Laboratory, University of Washington

Sep 01, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.85
BayesDel_addAF	Pathogenic	0.34	D
BayesDel_noAF	Pathogenic	0.25
Cadd	Uncertain	24
Dann	Uncertain	0.99
Eigen	Uncertain	0.67
Eigen_PC	Uncertain	0.59
FATHMM_MKL	Uncertain	0.87	D
M_CAP	Pathogenic	0.38	D
MetaRNN	Pathogenic	0.92	D;D
MetaSVM	Pathogenic	0.90	D
MutationTaster	Benign	1.0	D;D
PrimateAI	Uncertain	0.58	T
PROVEAN	Benign	-1.1	N;N
REVEL	Pathogenic	0.80
Sift	Uncertain	0.0010	D;D
Sift4G	Pathogenic	0.0	D;D
Vest4		0.93
MutPred		0.72		Loss of ubiquitination at K2630 (P = 0.093);Loss of ubiquitination at K2630 (P = 0.093);
MVP		0.99
MPC		0.17
ClinPred		0.95	D
GERP RS		4.5
gMVP		0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs80359014; hg19: chr13-32936733;