rs80358189

chr17-43074522-C-Achr17-43074522-C-Gchr17-43074522-C-T

Variant summary

Our verdict is Pathogenic. Variant got 22 ACMG points: 22P and 0B. PVS1 PM2 PP3_Strong PP5_Very_Strong

The NM_007294.4(BRCA1):c.4485-1G>T variant causes a splice acceptor 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. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: BRCA1 NM_007294.4 splice_acceptor
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic reviewed by expert panel P:7
• Conservation: PhyloP100: 2.00

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 22 ACMG points.

• PVS1: Splicing 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
• 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 17-43074522-C-A is Pathogenic according to our data. Variant chr17-43074522-C-A is described in ClinVar as [Pathogenic]. Clinvar id is 246501.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr17-43074522-C-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRCA1	NM_007294.4	c.4485-1G>T		splice_acceptor_variant		ENST00000357654.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRCA1	ENST00000357654.9	c.4485-1G>T		splice_acceptor_variant		1	NM_007294.4	P4

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 31

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:7

Revision: reviewed by expert panel

Submissions by phenotype

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

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 = 0.997462 -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	GeneKor MSA	Jan 01, 2020	This mutation occurs one base before exon 14 of the BRCA1 gene. This position is highly conserved in the human and other genomes and might be involved in mRNA processing. Therefore, this mutation is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant is also known as IVS13-1G>T or 4604-1G>T in the literature and it has been reported in a patient with high grade serous ovarian cancer(PMID: 26622941 ). The mutation database ClinVar contains entries for this variant (Variation ID: 246501). -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jan 19, 2021	Canonical splice site variant in a gene for which loss-of-function is a known mechanism of disease (Fleury 2015); Not observed in large population cohorts (Lek 2016); Also known as 4604-1G>T (IVS14-1G>T); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; This variant is associated with the following publications: (PMID: 26622941, 29446198, 31131967) -

Hereditary breast ovarian cancer syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Apr 20, 2023	Studies have shown that disruption of this splice site is associated with altered splicing resulting in multiple RNA products (PMID: 26622941). For these reasons, this variant has been classified as Pathogenic. Based on a multifactorial likelihood algorithm using genetic, in silico, and/or statistical data, this variant has been determined to have a high probability of being pathogenic (PMID: 31131967). ClinVar contains an entry for this variant (Variation ID: 246501). Disruption of this splice site has been observed in individual(s) with breast cancer and/or ovarian cancer (PMID: 12181777, 26622941, 27553291, 29446198, 34026625). This variant is not present in population databases (gnomAD no frequency). This sequence change affects an acceptor splice site in intron 13 of the BRCA1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in BRCA1 are known to be pathogenic (PMID: 20104584). -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jan 27, 2017	The c.4485-1G>T variant in BRCA1 has been reported in 1 French Canadian individu al with BRCA1-associated cancer (Fleury 2015). It was absent from large populati on studies. This variant occurs in the invariant region (+/- 1,2) of the splice consensus sequence and is predicted to cause altered splicing leading to an abno rmal or absent protein. Consistent with this prediction, in vitro functional stu dies demonstrate altered splicing and no appreciable protein expression in cells that harbor this variant in the homozygous state (Fleury 2015). In summary, the c.4485-1G>T variant meets criteria to be classified as pathogenic for hereditar y breast and ovarian cancer (HBOC) in an autosomal dominant manner based upon it s predicted impact to the protein and functional studies. -

Hereditary cancer-predisposing syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Mar 30, 2020

The c.4485-1G>T intronic pathogenic mutation results from a G to T substitution one nucleotide upstream from coding exon 13 of the BRCA1 gene. This alteration has been reported in a patient with high-grade serous epithelial ovarian cancer (EOC). In vivo studies conducted in an EOC cell line homozygous for this alteration identified the presence of a novel transcript induced by abnormal splicing, resulting in the absence of BRCA1 protein (Fleury H et al. Genes Cancer, 2015 Sep;6:378-398). This alteration has been reported in a large, worldwide study of BRCA1 and BRCA2 mutation carriers (Rebbeck TR et al. Hum. Mutat., 2018 05;39:593-620). This alteration was also identified in 2/50726 patients from an unselected population cohort from a single health system who underwent exome sequencing (Manickam K et al. JAMA Netw Open, 2018 09;1:e182140). 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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.14	T
BayesDel_noAF	Benign	-0.44
Cadd	Pathogenic	33
Dann	Benign	0.93
Eigen	Uncertain	0.62
Eigen_PC	Uncertain	0.34
FATHMM_MKL	Benign	0.73	D
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D
GERP RS		4.2

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.90
SpliceAI score (max)		0.96		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.67		Position offset: -30
DS_AL_spliceai		0.96		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: rs80358189; hg19: chr17-41226539;