17-43099773-A-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.547+2T>A variant causes a splice donor change. 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 (★★★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: BRCA1 NM_007294.4 splice_donor
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic reviewed by expert panel P:17
• Conservation: PhyloP100: 3.92

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 17-43099773-A-T is Pathogenic according to our data. Variant chr17-43099773-A-T is described in ClinVar as [Pathogenic]. Clinvar id is 37674.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr17-43099773-A-T is described in Lovd as [Pathogenic]. Variant chr17-43099773-A-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRCA1	NM_007294.4	c.547+2T>A		splice_donor_variant		ENST00000357654.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRCA1	ENST00000357654.9	c.547+2T>A		splice_donor_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:17

Revision: reviewed by expert panel

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 1 Pathogenic:8

Pathogenic, no assertion criteria provided	clinical testing	Sharing Clinical Reports Project (SCRP)	May 01, 2012	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genetics and Molecular Pathology, SA Pathology	Mar 01, 2022	The BRCA1:c.547+2T>A variant is classified as PATHOGENIC (ENIGMA criteria 2017) BRCA1:c.547+2T>A is a single nucleotide substitution in intron 8 at +2 bases from the last nucleotide of exon 8. BRCA1:c.547+2T>A is also described as IVS8+2T>A in the scientific literature using legacy nomenclature. This variant is predicted to effect aberrant splicing. Functional studies confirm BRCA1:c.547+2T>A results in skipping of exon 8 generating a frameshift transcript (BRCA1:r.442_547) that encodes premature termination of the protein synthesis (BRCA1:p.Gln148AspfsTer51) (Houdayer et al., 2012, PMID:22505045, Colombo et al., 2013, PMID:23451180). This variant has been reviewed by the ENIGMA expert review panel: ENIGMA determine BRCA1:c.547+2T>A as consistent with an IARC Class 5 variant equivalent to ACMG classification of Pathogenic. BRCA1:c.547+2T>A (rs80358047) is absent from population databases and is not on record in FLOSSIES. BRCA1:c.547+2T>A has been reported in multiple unrelated individuals with breast or ovarian cancer (Marchetti et al., 2018, PMID:30128899, Shattuck-Eidens et al., 1997 PMID:9333265, Trujillano et al., 2015 PMID:25556971). BRCA1:c.547+2T>A is on record in ClinVar (Variation ID:37674) reported by multiple clinical laboratories without conflict as pathogenic in association with Hereditary breast and ovarian cancer syndrome. This variant is listed in HGMD as ‘disease causing mutation’ in association with breast and/or ovarian cancer (Accession:CS973719). -
Pathogenic, criteria provided, single submitter	clinical testing	Counsyl	Nov 27, 2017	- -
Pathogenic, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA1)	May 29, 2002	- -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	May 11, 2023	- -
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)	Apr 03, 2016	Allele-specific assay on patient-derived mRNA demonstrated that the variant allele produces only predicted non-functional transcripts. Variant allele produces r.442_547del transcript (encoding predicted non-functional protein). -
Pathogenic, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Feb 10, 2022	- -

Hereditary cancer-predisposing syndrome Pathogenic:3

Pathogenic, criteria provided, single submitter	curation	Sema4, Sema4	Feb 28, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Sep 14, 2022	The c.547+2T>A intronic pathogenic mutation results from a T to A substitution two nucleotides after coding exon 6 in the BRCA1 gene. This nucleotide position is highly conserved in available vertebrate species. This alteration has been detected in numerous patients and families affected with breast and/or ovarian cancer (Pyne MT et al. Mutat. Res. 1999 Aug;406:101-7; Johnston JJ et al. Am. J. Hum. Genet. 2012 Jul;91:97-108; Tedaldi G et al. Oncotarget 2017 Jul;8:47064-47075; Marchetti C et al. Ann. Surg. Oncol. 2018 Nov;25(12):3701-3708; Cotrim DP et al. BMC Cancer. 2019 Jan;19(1):4). RNA studies have demonstrated that this alteration causes coding exon 6 skipping (total exon 8 in the literature), which results in a transcript that is subject to nonsense-mediated mRNA decay (Ambry internal data; Pyne MT et al. Mutat. Res. 1999 Aug;406:101-7; Houdayer C et al. Hum. Mutat. 2012 Aug;33:1228-38; Colombo M et al. PLoS ONE 2013 Feb;8:e57173). In silico splice site analysis predicts that this alteration will weaken the native splice donor site. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -
Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Feb 10, 2023	This variant causes a T to A nucleotide substitution at the +2 position of intron 7 of the BRCA1 gene. RNA studies have reported that the variant causes the out-of-frame skipping of exon 7, resulting in premature termination, in RNA derived from carriers and in a minigene splicing assay (PMID: 10479726, 22505045, 23451180, 24667779). This variant has been detected in at least seven individuals affected with breast or ovarian cancer (PMID: 10479726, 25452441, 27328445, 28423363, 30128899, 30606148; Color internal data). 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. -

Hereditary breast ovarian cancer syndrome Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Apr 23, 2023	ClinVar contains an entry for this variant (Variation ID: 37674). 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: 24667779). This variant is also known as IVS8+2T>A. Disruption of this splice site has been observed in individual(s) with breast and/or ovarian cancer (PMID: 9333265, 23940062, 25556971). This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 7 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, no assertion criteria provided	research	Biesecker Lab/Clinical Genomics Section, National Institutes of Health	Jul 13, 2012	- -
Pathogenic, no assertion criteria provided	research	Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto	Jan 31, 2014	- -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Mar 28, 2023	This variant disrupts a canonical splice-donor site and interferes with normal BRCA1 mRNA splicing. It has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). In the published literature, the variant has been reported in individuals with breast cancer (PMID: 23940062 (2013), 25452441 (2015), 25556971 (2015)) and ovarian cancer (PMID: 30606148 (2019), 25556971 (2015)). Published functional studies show that this variant causes aberrant mRNA splicing that result in skipping of exon 8 (PMID: 10479726 (1999), 22505045 (2012), 23451180 (2013), 24667779 (2014)). Based on the available information, this variant is classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Aug 03, 2020	Canonical splice site variant resulting in a null allele in a gene for which loss-of-function is a known mechanism of disease (Houdayer 2012, Colombo 2013, Steffensen 2014); Observed in multiple individuals with a personal and/or family history of breast and/or ovarian cancer (Shattuck-Eidens 1997, Turner 1999, Smith 2000, Grushko 2004, Johnston 2012, Colombo 2013); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; Not observed in large population cohorts (Lek 2016); Also known as c.666+2T>A or IVS8+2T>A; This variant is associated with the following publications: (PMID: 23940062, 9333265, 25556971, 23451180, 28423363, 27328445, 29346284, 30606148, 22703879, 26046366, 25525159, 22505045, 10479726, 24667779, 14760071, 10506595, 17284709, 11121624, 27600092, 29446198, 33287145) -

Breast and/or ovarian cancer Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario

Feb 23, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.18	D
BayesDel_noAF	Uncertain	0.020
Cadd	Pathogenic	27
Dann	Benign	0.97
Eigen	Pathogenic	0.90
Eigen_PC	Pathogenic	0.70
FATHMM_MKL	Uncertain	0.90	D
MutationTaster	Benign	1.0	A;A;A;A;A;A;A;A;A;A;A;A;A;A
GERP RS		5.2

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.90
SpliceAI score (max)		0.99		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.99		Position offset: 2

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

Publications

LitVar

Other links and lift over

dbSNP: rs80358047; hg19: chr17-41251790; COSMIC: COSV58804428; COSMIC: COSV58804428;