Our verdict is Pathogenic. The variant received 12 ACMG points: 12P and 0B. PVS1_ModeratePM2PP5_Very_Strong
The NM_007294.4(BRCA1):c.135-2A>G variant causes a splice acceptor, 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 pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★).
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]
BRCA1 Gene-Disease associations (from GenCC):
breast-ovarian cancer, familial, susceptibility to, 1
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, ClinGen, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
Our verdict: Pathogenic. The variant received 12 ACMG points.
PVS1
Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.013948498 fraction of the gene. Cryptic splice site detected, with MaxEntScore 3.1, offset of 28, new splice context is: tgctgaaacttctcaaccAGaag. Cryptic site results in frameshift change. If cryptic site found is not functional and variant results in exon loss, it results in inframe change.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 17-43106535-T-C is Pathogenic according to our data. Variant chr17-43106535-T-C is described in ClinVar as Pathogenic. ClinVar VariationId is 125567.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_007294.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
Selected
Gene
Transcript
Tags
HGVSc
HGVSp
Effect
Exon Rank
Protein
UniProt
BRCA1
NM_007294.4
MANE Select
c.135-2A>G
splice_acceptor intron
N/A
NP_009225.1
BRCA1
NM_001407581.1
c.135-2A>G
splice_acceptor intron
N/A
NP_001394510.1
BRCA1
NM_001407582.1
c.135-2A>G
splice_acceptor intron
N/A
NP_001394511.1
Ensembl Transcripts
Selected
Gene
Transcript
Tags
HGVSc
HGVSp
Effect
Exon Rank
Protein
UniProt
BRCA1
ENST00000357654.9
TSL:1 MANE Select
c.135-2A>G
splice_acceptor intron
N/A
ENSP00000350283.3
BRCA1
ENST00000471181.7
TSL:1
c.135-2A>G
splice_acceptor intron
N/A
ENSP00000418960.2
BRCA1
ENST00000470026.6
TSL:1
c.135-2A>G
splice_acceptor intron
N/A
ENSP00000419274.2
Frequencies
GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
26
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00
Hom.:
0
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:8
Revision: criteria provided, multiple submitters, no conflicts
Breast-ovarian cancer, familial, susceptibility to, 1Pathogenic:2
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
Nov 25, 2004
Breast Cancer Information Core (BIC) (BRCA1)
Significance:Pathogenic
Review Status:no assertion criteria provided
Collection Method:clinical testing
not providedPathogenic:2
Jan 01, 2020
GeneKor MSA
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing
This variation occurs 2 nucleotides before exon 5 of the BRCA1 gene. This position is highly conserved in the human and other genomes and is crucial in mRNA processing. This mutation is expected to result in incorrect splicing, alteration in the reading frame and a truncated protein. This variant is not listed in population databases (ExAC, 1000 genomes) and the mutation database ClinVar contains an entry for this variant (Variation ID: 125567).
Department of Pathology and Laboratory Medicine, Sinai Health System
Significance:Pathogenic
Review Status:no assertion criteria provided
Collection Method:clinical testing
The c.135-2A>G variant was not identified in the literature but was identified in the BIC database (1x) as clinically important. This variant is predicted to cause abnormal splicing because the nucleotide substitution occurs in the -2 position of the splice consensus sequence. In addition, in-silico or computational prediction software (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predicts abolishment of the consensus splice site in 5 of 5 different programs. In summary, this splice site variant in the BRCA1 gene is the type of variant expected to cause hereditary breast and ovarian cancer and is classified as pathogenic.
This variant causes an A to G nucleotide substitution at the -2 position of intron 3 of the BRCA1 gene. RNA studies have reported that this variant causes splicing defects expected to disrupt protein expression or result in in-frame deletion impacting the functionally important RING domain (PMID: 19471317; ClinVar SCV000608079.5). A functional study has reported that this splicing variant impacts BRCA1 function in a haploid cell proliferation assay (PMID: 30209399). This variant has been reported in several individuals and families affected with breast and ovarian cancer (PMID: 25682074, 28692638, 28724667, 29176636, 29446198, 30078507, 31159747, 31954625). And a multifactorial analysis also has reported a likelihood ratio for pathogenicity based on personal and family history of 1.34 from log(LR)=0.127201542 for one carrier (PMID: 31853058). 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.
Apr 30, 2021
Ambry Genetics
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing
The c.135-2A>G intronic pathogenic mutation (also known as IVS4-2A>G) results from an A to G substitution two nucleotides upstream from coding exon 3 in the BRCA1 gene. This alteration is present in many patients from diverse ethnic backgrounds who are affected by breast and/or ovarian cancer (Tsaousis GN et al. BMC Cancer, 2019 Jun;19:535; Arai M et al. J Hum Genet, 2018 Apr;63:447-457; Rebbeck TR et al. Hum Mutat, 2018 05;39:593-620; Li A et al. Gynecol Oncol, 2018 10;151:145-152; Sun J et al. Clin Cancer Res, 2017 Oct;23:6113-6119; Wong-Brown MW et al. Breast Cancer Res Treat, 2015 Feb;150:71-80). RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested, and may be a combination of deleterious exon skipping and a partial intron retention event (Ambry internal data; Caux-Moncoutier V, Eur. J. Hum. Genet. 2009 Nov; 17(11):1471-80). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.
Hereditary breast ovarian cancer syndromePathogenic:2
Sep 20, 2023
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing
Experimental studies have shown that disruption of this splice site affects BRCA1 function (PMID: 30209399). For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the BRCA1 protein in which other variant(s) (p.Cys61Gly) have been determined to be pathogenic (PMID: 7894493, 9525870, 11278247, 19594371, 19770520, 22172724). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. Studies have shown that disruption of this splice site results in skipping of exon 4, but is expected to preserve the integrity of the reading-frame (Invitae). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. ClinVar contains an entry for this variant (Variation ID: 125567). Disruption of this splice site has been observed in individual(s) with breast and/or ovarian cancer (PMID: 25682074, 28724667, 29176636, 30078507, 31825140). This variant is not present in population databases (gnomAD no frequency). This sequence change affects an acceptor splice site in intron 3 of the BRCA1 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and likely results in a shortened protein product.
Sep 09, 2024
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing
Variant summary: BRCA1 c.135-2A>G 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. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing and loss of BRCA1 function. The variant was absent in 248196 control chromosomes. c.135-2A>G has been reported in the literature in individuals affected with Hereditary Breast And Ovarian Cancer Syndrome (example: Rebbeck_2018). At least one functional study reports experimental evidence evaluating an impact on protein function and showed a damaging effect of this variant on homology directed repair (HDR) activity (e.g. Findlay_2018). The following publications have been ascertained in the context of this evaluation (PMID: 30209399, 29446198). ClinVar contains an entry for this variant (Variation ID: 125567). Based on the evidence outlined above, the variant was classified as pathogenic.