rs273899695

Positions:

• chr17-43104262-CT-C

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_007294.4(BRCA1):​c.302-2del variant causes a splice acceptor change. The variant allele was found at a frequency of 0.00000249 in 1,608,590 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★★).

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: BRCA1 NM_007294.4 splice_acceptor
• Clinical Significance: Pathogenic reviewed by expert panel P:13
• Conservation: PhyloP100: 4.30

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 18 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift change.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 17-43104262-CT-C is Pathogenic according to our data. Variant chr17-43104262-CT-C is described in ClinVar as [Pathogenic]. Clinvar id is 54753.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr17-43104262-CT-C is described in Lovd as [Pathogenic]. Variant chr17-43104262-CT-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRCA1	NM_007294.4	c.302-2del		splice_acceptor_variant		ENST00000357654.9	NP_009225.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BRCA1	ENST00000357654.9	c.302-2del		splice_acceptor_variant		1	NM_007294.4	ENSP00000350283	P4

Frequencies

GnomAD3 genomes AF: 0.00000658 AC: 1 AN: 152034 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

GnomAD4 exome AF: 0.00000206 AC: 3 AN: 1456556 Hom.: 0 Cov.: 33 AF XY: 0.00000276 AC XY: 2 AN XY: 724900

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: 0.0000332

GnomAD4 genome AF: 0.00000658 AC: 1 AN: 152034 Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1 AN XY: 74264

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00

Bravo AF: 0.00000378

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:13

Revision: reviewed by expert panel

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 1 Pathogenic:4

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)	May 29, 2002	- -
Pathogenic, no assertion criteria provided	clinical testing	Sharing Clinical Reports Project (SCRP)	Mar 14, 2013	- -
Pathogenic, criteria provided, single submitter	clinical testing	Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge	Oct 02, 2015	- -

Hereditary breast ovarian cancer syndrome Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Oct 28, 2019	Variant summary: BRCA1 c.302-2delA is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Five predict the variant abolishes a canonical 3 acceptor site and two predict it creates/strengthens a cryptic exonic 3 acceptor site. These predictions are supported by analysis of cDNA products demonstrating that the variant activates a cryptic splicing site which results in a 10-bp frameshift deletion at the beginning of exon 6 causing the addition of 14 new residues and resulting in a premature stop codon (Chen_2006). c.302-2delA has been reported in the literature in multiple individuals affected with Hereditary Breast and Ovarian Cancer (Tesoriero_2005, Borg_2010, Rebbeck_2018). These data indicate that the variant is very likely to be associated with disease. Six ClinVar submitters (evaluation after 2014) cite 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	- -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Sep 15, 2022	For these reasons, this variant has been classified as Pathogenic. Studies have shown that disruption of this splice site alters mRNA splicing and is expected to lead to the loss of protein expression (PMID: 12815598, 16619214). ClinVar contains an entry for this variant (Variation ID: 54753). This variant is also known as 421-2delA and IVS6-2delA. Disruption of this splice site has been observed in individual(s) with breast and ovarian cancer (PMID: 9333265, 10486320, 12815598, 16619214, 20104584). This variant is not present in population databases (gnomAD no frequency). This sequence change affects a splice site in intron 5 of the BRCA1 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or disrupted protein product. -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Mar 16, 2018	The c.302-2delA variant in BRCA1 has been reported in at least 16 individuals wi th breast and/or ovarian cancer (Shattuck-Eidens 1997, Gayther 1999, Southey 200 3, Chen 2006, Borg 2010, BIC database [https://research.nhgri.nih.gov/bic/]) and segregated with disease in at least 9 affected relatives from 1 family (Southey 2003). This variant has also been reported by other clinical laboratories in C linVar (Variation ID# 54753) and was absent from large population databases. Th e c.302-2delA variant occurs in the invariant region (+/- 1,2) of the splice con sensus sequence and is predicted to cause altered splicing leading to an abnorma l or absent protein. In vitro studies as well as sequencing of cDNA from individ uals with this variant showed that it leads to activation of a cryptic splice si te, leading to 10 bp frameshift at the beginning of the next exon and resulting in the addition of 14 new amino acid residues and a premature stop codon (Chen 2 006). In summary, this variant meets criteria to be classified as pathogenic for hereditary breast and ovarian cancer (HBOC) in an autosomal dominant manner bas ed upon presence in multiple affected individuals, segregation studies, absence from the general population, functional evidence, and predicted impact on the pr otein. ACMG/AMP Criteria applied (Richards 2015): PVS1, PS4, PP1_Strong. -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Nov 17, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Mar 12, 2024	Canonical splice site variant demonstrated to result in aberrant splicing leading to a predicted null allele in a gene for which loss-of-function is a known mechanism of disease (PMID: 12815598, 16619214); Observed in several individuals with personal and/or family history consistent with pathogenic variants in this gene (PMID: 9333265, 10486320, 12815598, 16211554, 16619214, 33758026); Not observed at significant frequency in large population cohorts (gnomAD); Multifactorial likelihood analysis suggests this variant is pathogenic (PMID: 31131967); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; Also known as 421-2delA and IVS6-2delA; This variant is associated with the following publications: (PMID: 10486320, 12815598, 9333265, 16211554, 21702907, 16619214, 18712473, 31447099, 30787465, 33087929, 33758026, 31131967) -

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Sep 28, 2021	This variant causes deletion of the nucleotide at the -2 position of intron 5 of the BRCA1 gene. RNA studies found the variant to activate a cryptic splice acceptor site leading to a 10bp frameshift, premature truncation, and nonsense-mediated decay (PMID: 12815598, 16619214). This variant has been observed in individuals affected with breast and/or ovarian cancer (PMID: 9333265, 10486320, 12815598, 16211554, 16619214, 20104584) and has been identified in 22 families among CIMBA participants (PMID: 29446198). In one large pedigree, this variant was found to segregate with breast cancer, ovarian cancer, and melanoma in at least 9 affected individuals (PMID: 12815598). 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	Sep 15, 2021	The c.302-2delA intronic pathogenic mutation results from the deletion of one nucleotide two nucleotides upstream from coding exon 5 of the BRCA1 gene. This mutation has been described in multiple families with hereditary breast and ovarian cancer (HBOC) syndrome (Shattuck-Eidens D et al. JAMA. 1997 Oct;278:1242-50; Gayther SA et al. Am. J. Hum. Genet. 1999 Oct;65:1021; Tesoriero AA et al. Hum. Mutat. 2005 Nov;26:495; Borg A et al. Hum. Mutat. 2010 Mar;31:E1200-40; Rebbeck TR et al. Hum. Mutat. 2018 May;39:593-620). RNA studies have also demonstrated that this alteration results in an aberrant transcript that results in the deletion of 10 base pairs from coding exon 5 and results in a frameshift (Ambry internal data; Chen X et al. Hum. Mutat. 2006 May;27:427-35; Southey MC et al. Hum. Mutat. 2003 Jul;22:86-91). This alteration was classified as pathogenic in a multifactorial model of variant interpretation that incorporates co-segregation, family history, co-occurrence, tumor pathology, and case-control data (Parsons MT et al. Hum. Mutat. 2019 09;40(9):1557-1578). Of note, this alteration is also designated as 421-2delA and IVS6-2delA in published literature. In addition to the clinical data presented in the literature, alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as a disease-causing mutation. -

Breast and/or ovarian cancer Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Foulkes Cancer Genetics LDI, Lady Davis Institute for Medical Research

Aug 22, 2011

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		1.0		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.99		Position offset: -11
DS_AL_spliceai		1.0		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: rs273899695; hg19: chr17-41256279;