17-43104968-T-C

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM2 PP3 PP5_Very_Strong

The NM_007294.4(BRCA1):c.213-12A>G variant causes a splice polypyrimidine tract, 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. Variant has been reported in ClinVar as Pathogenic (★★★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: BRCA1 NM_007294.4 splice_polypyrimidine_tract, intron
• Scores: Splicing: ADA: 0.9981
• Clinical Significance: Pathogenic reviewed by expert panel P:28
• Conservation: PhyloP100: 0.312

Genes affected

BRCA1 (HGNC:1100): (BRCA1 DNA repair associated) This gene encodes a 190 kD nuclear phosphoprotein that plays a role in maintaining genomic stability, and it also acts as a tumor suppressor. The BRCA1 gene contains 22 exons spanning about 110 kb of DNA. The encoded protein combines with other tumor suppressors, DNA damage sensors, and signal transducers to form a large multi-subunit protein complex known as the BRCA1-associated genome surveillance complex (BASC). This gene product associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. This protein thus plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. Alternative splicing plays a role in modulating the subcellular localization and physiological function of this gene. Many alternatively spliced transcript variants, some of which are disease-associated mutations, have been described for this gene, but the full-length natures of only some of these variants has been described. A related pseudogene, which is also located on chromosome 17, has been identified. [provided by RefSeq, May 2020]

ACMG classification

Verdict is Pathogenic. Variant got 11 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 17-43104968-T-C is Pathogenic according to our data. Variant chr17-43104968-T-C is described in ClinVar as [Pathogenic]. Clinvar id is 37450.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr17-43104968-T-C is described in Lovd as [Likely_pathogenic]. Variant chr17-43104968-T-C is described in Lovd as [Pathogenic]. Variant chr17-43104968-T-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRCA1	NM_007294.4	c.213-12A>G		splice_polypyrimidine_tract_variant, intron_variant		ENST00000357654.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRCA1	ENST00000357654.9	c.213-12A>G		splice_polypyrimidine_tract_variant, intron_variant		1	NM_007294.4	P4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

Alfa AF: 0.0000595 Hom.: 0

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:28

Revision: reviewed by expert panel

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 1 Pathogenic:10

Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Aug 24, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Counsyl	Dec 09, 2015	- -
Pathogenic, criteria provided, single submitter	clinical testing	Michigan Medical Genetics Laboratories, University of Michigan	Nov 03, 2014	- -
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, reviewed by expert panel	curation	Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)	Jun 18, 2019	IARC class based on posterior probability from multifactorial likelihood analysis, thresholds for class as per Plon et al. 2008 (PMID: 18951446). Class 5 based on posterior probability = 1 -
Pathogenic, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA1)	Dec 30, 1999	- -
Pathogenic, no assertion criteria provided	clinical testing	BRCAlab, Lund University	Aug 26, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München	Jul 08, 2022	- -
Pathogenic, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Sharing Clinical Reports Project (SCRP)	Jun 06, 2012	- -

not provided Pathogenic:8

Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Oct 20, 2020	In the published literature, this variant has been reported in multiple families affected with hereditary breast and/or ovarian cancer as well as individuals affected with pancreatic and endometrial cancers (PMIDs: 9805131 (1998), 11802209 (2002), 16683254 (2006), 18627636 (2008), 23164213 (2012), 23479189 (2013), 25863477 (2015), 25971625 (2015), 28528518 (2017), and 29360161 (2018)). In addition, this variant is described in the published literature as interfering with normal splicing of the BRCA1 mRNA by activating a cryptic splice site and causing the inclusion of 11 base pairs of intronic sequence in the BRCA1 mRNA. The inclusion of this intronic sequence alters the translation reading frame of the BRCA1 mRNA and is predicted to cause the synthesis of a truncated BRCA1 protein (PMID: 23164213 (2012), 21735045 (2012), and 9805131 (1998)). -
Pathogenic, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The BRCA1 c.213-12A>G variant was identified in 6 of 11748 proband chromosomes (frequency: 0.0005) from Spanish, Korean, German, Austrian, Malayasian and Dutch individuals or families with high risk breast and ovarian cancer, or triple negative breast cancer (de Juan Jimenez_2013_23479189, Kang_2015_25863477, Meindl_2002_11802209, Muendlein_2015_25971625, Thirthagiri_2008_18627636, van der Hout_2006_16683254). One case report describes a patient diagnosed with endometrial cancer at 46 and a triple negative breast cancer at 33 as carrying two pathogenic mutations BRCA1 c.213-12A>G, p.Arg71SerfsX21 and MSH6 c.515_516insT, p.Ile172fsX10 (Kast_2012_ 23164213). The c.213-12A>G 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. The variant was initially identified in a family with a history of breast cancer, segregating with the disease, and RT-PCR analysis on whole blood lymphocyte showed an 11 nucleotide insert at the intron 4/exon 6 boundary leading to a frameshift and truncated protein (Hoffman_1998_ 9805131). The variant was also identified in dbSNP (ID: rs80358163) “With Pathogenic allele”, ClinVar (classified pathogenic (last evaluated 2017); submitters: pathogenic by Ambry Genetics, GeneDx, Michigan Medical Genetics Laboratories (University of Michigan), Laboratory for Molecular Medicine (Partners HealthCare Personalized Medicine), Quest Diagnostics Nichols Institute San Juan Capistrano, CIMBA, Counsyl, Invitae, SCRP, BIC ), Clinvitae (4x), GeneInsight-COGR (as pathogenic by 3 clinical laboratories ), BIC Database (25x with clinical importance, classification pending), ARUP Laboratories (5-definitely pathogenic), Zhejiang Colon Cancer Database (1x) and was not identified in Cosmic, MutDB, LOVD 3.0, UMD-LSDB, the 1000 Genomes Project, the NHLBI GO Exome Sequencing Project, the Exome Aggregation Consortium (August 8th 2016), or the Genome Aggregation Database (Feb 27, 2017). 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	PreventionGenetics, part of Exact Sciences	Jun 29, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Jan 27, 2023	PP5, PM2, PS3, PS4_moderate -
Pathogenic, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Feb 21, 2023	Non-canonical splice site variant demonstrated to result in loss-of-function (Hoffman et al., 1998; Menndez et al., 2012); Not observed at significant frequency in large population cohorts (gnomAD); Observed in individuals with a personal and family history consistent with pathogenic variants in this gene (Hoffman et al., 1998; Meindl et al., 2002; Thirthagiri et al., 2008; Foretova et al., 2010; de Juan Jimenez et al., 2013; Kang et al., 2015); Multifactorial likelihood analysis suggests this variant is pathogenic (Parsons et al., 2019); Also known as 332-12A>G or IVS5-12A>G; This variant is associated with the following publications: (PMID: 15024741, 21394499, 27836010, 28528518, 31492746, 11802209, 18627636, 23479189, 9805131, 24285858, 23164213, 25863477, 26681312, 26659639, 27221827, 28324225, 29360161, 28993434, 30702160, 30093976, 30875412, 31825140, 21735045, 31131967) -
Pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -

Hereditary breast ovarian cancer syndrome Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 19, 2024	This sequence change falls in intron 4 of the BRCA1 gene. It does not directly change the encoded amino acid sequence of the BRCA1 protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with breast and/or ovarian cancer (PMID: 9805131, 19563646, 21348412, 23479189). It has also been observed to segregate with disease in related individuals. This variant is also known as IVS5-12A>G. ClinVar contains an entry for this variant (Variation ID: 37450). Studies have shown that this variant results in activation of a cryptic splice site and introduces a premature termination codon (PMID: 9805131; Invitae). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jan 19, 2016	The c.213-12A>G variant in BRCA1 has been reported in >25 individuals with BRCA1 -associated cancers and segregated with disease in 4 affected relatives from 2 f amilies (Dong 1998, Hoffman 1998, Meindl 2002, Thirthagiri 2008, Kast 2012, de J uan Jimenez 2013, Brohet 2014,Breast Cancer Information Core (BIC) database). Th is variant was absent from large population studies. In vitro functional studies provide evidence that the c.213-12A>G variant introduces a cryptic splice site, causing an additional 11 nucleotides to be retained and leading to a frameshift , which alters the protein?s amino acid sequence beginning at position 71 and le ads to a premature termination codon 21 amino acids downstream (Hoffman 1998, Me nendez 2012). This alteration is then predicted to lead to a truncated or absent protein. Heterozygous loss of function of the BRCA1 gene is an established dise ase mechanism in hereditary breast and ovarian cancer (HBOC). In summary, this v ariant meets our criteria to be classified as pathogenic for HBOC in an autosoma l dominant manner based upon segregation studies, absence from controls, and fun ctional evidence. -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Apr 23, 2022	Variant summary: BRCA1 c.213-12A>G alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Two predict the variant abolishes the canonical 3' splice acceptor site. Two predict the variant creates a new 3' acceptor site at position -12. At least one publication reports experimental evidence that this variant affects mRNA splicing by incorporation of 11 bases of intron 5 leading to a frameshift in the codon sequence (Hoffman_1998). The variant was absent in 250918 control chromosomes. c.213-12A>G has been reported in the literature in multiple individuals affected with Hereditary Breast And Ovarian Cancer Syndrome (example, Rebbeck_2018). These data indicate that the variant is very likely to be associated with disease. Multiple clinical diagnostic laboratories, an expert panel (ENIGMA) and a consortium (CIMBA) have submitted clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic. Based on the evidence outlined above, the variant was 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	Jan 10, 2023	This variant causes an A to G nucleotide substitution at the -12 position of intron 4 of the BRCA1 gene. An RNA study has shown that this variant causes new splice acceptor that inserts 11 bp at the beginning of exon 6, resulting in frameshift and premature truncation within exon 6 (PMID: 9805131). This variant has been reported in at least six individuals and multiple families affected with breast or ovarian cancer (PMID: 9760198, 9805131, 18627636, 21147080, 25863477, 25971625, 28528518), and in an individual affected with pancreatic and ovarian cancer (PMID: 29360161). A multifactorial analysis has reported likelihood ratios for pathogenicity based on segregation and tumor pathology of 29429 and 1132, respectively (PMID: 31131967). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of BRCA1 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Mar 08, 2022	The c.213-12A>G intronic pathogenic mutation results from an A to G substitution 12 nucleotides upstream from coding exon 4 in the BRCA1 gene. This alteration has been reported in numerous individuals with personal and/or family history of breast and/or ovarian cancers (Meindl A et al. Int. J. Cancer, 2002 Feb;97:472-80; Thirthagiri E et al. Breast Cancer Res., 2008 Jul;10:R59; de Juan Jiménez I et al. Fam. Cancer. 2013 Dec;12:767-77; Brohet RM et al. J. Med. Genet., 2014 Feb;51:98-107; Kang E et al. Breast Cancer Res. Treat., 2015 May;151:157-68; Meisel C et al. Arch. Gynecol. Obstet. 2017 May;295:1227-1238; Cock-Rada AM et al. Fam. Cancer. 2018 Jan;17:23-30; Wen WX et al. J. Med. Genet., 2018 Feb;55:97-103; Dudley B et al. Cancer, 2018 Apr;124:1691-1700). In one 11-person family with early-onset breast cancer this mutation was shown to segregate with disease (Hoffman JD et al. Am. J. Med. Genet. 1998 Nov;80(2):140-4). This alteration results in the formation of a cryptic splice acceptor site, leading to an insertion of 11 nucleotides with a predicted premature termination codon (Ambry internal data; Hoffman JD et al. Am. J. Med. Genet. 1998 Nov;80(2):140-4; Menedez M et al. Breast Cancer Res. Treat. 2012 Apr;132(3):979-92). Of note, this mutation is also designated as IVS5-12A>G in published literature. Based on the available evidence, this alteration is classified as a pathogenic mutation. -

not specified Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Feb 10, 2017

- -

Breast and/or ovarian cancer Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

CZECANCA consortium

Jun 11, 2019

- -

Neoplasm of ovary Pathogenic:1

Pathogenic, no assertion criteria provided

research

German Consortium for Hereditary Breast and Ovarian Cancer, University Hospital Cologne

Dec 01, 2018

- -

Familial cancer of breast;C2676676:Breast-ovarian cancer, familial, susceptibility to, 1;C3280442:Pancreatic cancer, susceptibility to, 4;C4554406:Fanconi anemia, complementation group S Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Sep 23, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
Cadd	Benign	18
Dann	Benign	0.88

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.97
SpliceAI score (max)		0.68		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.33		Position offset: -1
DS_AL_spliceai		0.68		Position offset: -12

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

Publications

LitVar

Other links and lift over

dbSNP: rs80358163; hg19: chr17-41256985;