rs80358086

chr17-43070922-A-Cchr17-43070922-A-Gchr17-43070922-A-T

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.4986+6T>G variant causes a splice donor region, intron change. 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_donor_region, intron
• Scores: Splicing: ADA: 0.9983
• Clinical Significance: Pathogenic reviewed by expert panel P:17 O:2
• Conservation: PhyloP100: 5.03

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 17-43070922-A-C is Pathogenic according to our data. Variant chr17-43070922-A-C is described in ClinVar as [Pathogenic]. Clinvar id is 55344.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr17-43070922-A-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRCA1	NM_007294.4	c.4986+6T>G		splice_donor_region_variant, intron_variant		ENST00000357654.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRCA1	ENST00000357654.9	c.4986+6T>G		splice_donor_region_variant, intron_variant		1	NM_007294.4	P4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000400 AC: 1 AN: 249776 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 135148

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000892

Gnomad OTH exome AF: 0.00

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:17 Other:2

Revision: reviewed by expert panel

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 1 Pathogenic:8 Other: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, no assertion criteria provided	clinical testing	Sharing Clinical Reports Project (SCRP)	Jul 23, 2012	- -
not provided, no classification provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA1)	-	- -
Pathogenic, no assertion criteria provided	clinical testing	BRCAlab, Lund University	Mar 02, 2020	- -
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 = 0.999999 -
Likely pathogenic, criteria provided, single submitter	clinical testing	Counsyl	Jul 14, 2017	- -
not provided, no classification provided	in vitro	Brotman Baty Institute, University of Washington	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Sep 13, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine	Feb 05, 2019	This c.4986+6T>G variant in the BRCA1 gene has been reported in multiple individuals affected with breast cancer or ovarian cancer (PMID 11179017, 16619214, 21913181, 22160602) and is extremely rare in general population databases. An RT-PCR assay using mRNA derived from an affected individual showed 65bp insertion, which is predicted to introduce a premature translation termination codon (PMID 16619214). Therefore, the c.4986+6T>G variant in the BRCA1 gene is classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Aug 28, 2023	This variant causes a T>G nucleotide substitution at the +6 position of intron 15 of the BRCA1 gene. This variant is also known as 5105+6T>G and IVS16+6T>G in the literature. RNA studies on carrier-derived RNA (PMID: 16619214) and in a mini-gene splicing assay (PMID: 24667779) have found this variant to disrupt splicing in a manner that is expected to result in an absent or non-functional protein product. This variant has been reported to be loss-of-function in a haploid cell proliferation assay (PMID: 30209399). This variant has been reported in individuals with personal and/or family history of breast and ovarian cancer (PMID: 11179017, 16619214, 21913181, 22160602). This variant also has been reported as pathogenic in a multifactorial analysis based in part to segregation and tumor pathology likelihood ratios of 18.9 and 1134.1, respectively (PMID: 31131967). This variant has been identified in 1/249776 chromosomes 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. -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Oct 07, 2015	This variant is denoted BRCA1 c.4986+6T>G or IVS15+6T>G and consists of a T>G nucleotide substitution at the +6 position of intron 15 of the BRCA1 gene. Multiple in silico models predict this variant to weaken the nearby natural donor site, and to possibly cause abnormal gene splicing. An RT-PCR study reported that this variant is associated with aberrant splicing, and leads to a 65bp insertion and a predicted stop codon (Chen 2006). This variant, also denoted BRCA1 5105+6T>G and IVS16+6T>G using alternate nomenclature, has been reported in association with breast and ovarian cancer (Risch 2001, Chen 2006, Zhang 2011, Litton 2012, Schneegans 2012). Based on the currently available information, we consider BRCA1 c.4986+6T>G to be a pathogenic variant. -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Dec 14, 2022	- -

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Oct 10, 2023	The c.4986+6T>G intronic pathogenic mutation variant results from a T to G substitution 6 nucleotides after coding exon 14 in the BRCA1 gene. This alteration has been reported in multiple families with hereditary breast and/or ovarian cancer (Risch HA et al. Am. J. Hum. Genet. 2001 Mar;68:700-10; Schneegans SM et al. Fam. Cancer. 2012 Jun;11:181-8; Schubert S et al. Int. J. Cancer 2019 Jun;144(11):2683-2694; Rebbeck TR et al. Hum. Mutat. 2018 05;39(5):593-620). RNA splicing analyses have shown this alteration to result in aberrant splicing that results in the insertion of 65 nucleotides and results in nonsense-mediated mRNA decay (Ambry internal data; Chen X et al. Hum. Mutat. 2006 May;27:427-35; Steffensen AY et al. Eur. J. Hum. Genet. 2014 Dec;22:1362-8). Another functional study found that this nucleotide substitution is deleterious in a high throughput genome editing haploid cell survival assay (Findlay GM et al. Nature 2018 10;562(7726):217-222). In addition, this alteration was also classified as Pathogenic in a multifactorial model of variant interpretation that incorporates co-segregation, family history, co-occurrence and tumor pathology and case-control data (Parsons MT et al. Hum Mutat. 2019 Sep;40(9):1557-1578). Of note, this alteration is also referred to as 5105+6T>G and IVS16+6T>G in the published literature. 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	Jul 07, 2023	This variant causes a T>G nucleotide substitution at the +6 position of intron 15 of the BRCA1 gene. This variant is also known as 5105+6T>G and IVS16+6T>G in the literature. RNA studies on carrier-derived RNA (PMID: 16619214) and in a mini-gene splicing assay (PMID: 24667779) have found this variant to disrupt splicing in a manner that is expected to result in an absent or non-functional protein product. This variant has been reported to be loss-of-function in a haploid cell proliferation assay (PMID: 30209399). This variant has been reported in individuals with personal and/or family history of breast and ovarian cancer (PMID: 11179017, 16619214, 21913181, 22160602). This variant also has been reported as pathogenic in a multifactorial analysis based in part to segregation and tumor pathology likelihood ratios of 18.9 and 1134.1, respectively (PMID: 31131967). This variant has been identified in 1/249776 chromosomes 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:2

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	Invitae	Dec 18, 2023	This sequence change falls in intron 15 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 present in population databases (rs80358086, gnomAD 0.0009%). This variant has been observed in individual(s) with breast and/or ovarian cancer (PMID: 11179017, 16619214, 21913181, 22160602). ClinVar contains an entry for this variant (Variation ID: 55344). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant alters mRNA splicing and is expected to lead to the loss of protein expression (PMID: 16619214, 24667779, 30209399; Invitae). This variant disrupts the c.4986+6T nucleotide in the BRCA1 gene. Other variant(s) that disrupt this nucleotide have been determined to be pathogenic (PMID: 10406662, 21120943, 21324516, 21965345, 24729269). This suggests that this nucleotide is clinically significant, and that variants that disrupt this position are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -

Breast and/or ovarian cancer Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

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

Mar 08, 2017

- -

Malignant tumor of breast Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

-

The c.4986+6T>G variant has been previously reported in the literature in 1 out of 1298 proband chromosomes, in an individual with ovarian cancer (Risch 2001). The variant has also been identified by our laboratory in one family where the variant was demonstrated to segregate with disease in 5 affected family members with breast cancer, suggesting this variant is pathogenic. In the UMD, BIC and LOVD databases, an intronic mutation at the same genomic location but with a different base alteration (IVS16+16 T>C) was described as being a deleterious mutation that creates an aberrant transcript by activating a cryptic splice donor site. It is listed in the dbSNP database (rs80358086) but no frequency information was provided and so the population frequency could not be assessed. The variant is located in the 5' splice region but does not affect the highly conserved +1 and +2 positions. However, positions +3 to +6 are part of the splicing consensus sequence and variants involving these positions sometimes affect splicing. In summary, based on above information, this variant is classified as pathogenic. -

Breast carcinoma Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Medical Genetics Laboratory, Umraniye Training and Research Hospital, University of Health Sciences

Aug 08, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
Cadd	Benign	23
Dann	Benign	0.93

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.89
SpliceAI score (max)		0.83		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.35		Position offset: 0
DS_DL_spliceai		0.83		Position offset: 6

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

Publications

LitVar

Other links and lift over

dbSNP: rs80358086; hg19: chr17-41222939;