17-43070925-C-G

Variant names:

• chr17-43070925-C-G
• rs80358023
• NM_007294.4:c.4986+3G>C

Variant summary

Our verdict is Pathogenic. The variant received 11 ACMG points: 11P and 0B. PM2 PP3 PP5_Very_Strong

The NM_007294.4(BRCA1):​c.4986+3G>C variant causes a splice region, 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 benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: BRCA1 NM_007294.4 splice_region, intron
• Scores: Splicing: ADA: 0.9949
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:22 O:1
• Conservation: PhyloP100: 0.229

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

Our verdict: Pathogenic. The variant received 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 17-43070925-C-G is Pathogenic according to our data. Variant chr17-43070925-C-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 55341.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-43070925-C-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRCA1	NM_007294.4	c.4986+3G>C		splice_region_variant, intron_variant	Intron 15 of 22	ENST00000357654.9	NP_009225.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRCA1	ENST00000357654.9	c.4986+3G>C		splice_region_variant, intron_variant	Intron 15 of 22	1	NM_007294.4	ENSP00000350283.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:22 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 1 Pathogenic:7 Other:1

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

- -

Mar 02, 2020

BRCAlab, Lund University

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

-

Brotman Baty Institute, University of Washington

Significance: not provided

Review Status: no classification provided

Collection Method: in vitro

- -

Mar 05, 2024

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 13, 2015

Counsyl

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: literature only

- -

Apr 02, 2020

Department of Molecular Diagnostics, Institute of Oncology Ljubljana

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Aug 11, 2022

MGZ Medical Genetics Center

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

May 29, 2002

Breast Cancer Information Core (BIC) (BRCA1)

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not provided Pathogenic:5

Jun 30, 2018

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Oct 23, 2020

Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 02, 2018

GeneDx

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is denoted BRCA1 c.4986+3G>C or IVS15+3G>C and consists of a G>C nucleotide substitution at the +3 position of intron 15 of the BRCA1 gene. This variant is also known as BRCA1 5105+3G>C or IVS16+3G>C using alternate nomenclature. In vitro RNA analysis demonstrated that this variant causes aberrant splicing, resulting in an out-of-frame intron inclusion predicted to result in protein truncation (Wappenschmidt 2012). This variant has been observed in multiple individuals with a personal and/or family history of breast, ovarian, and/or pancreatic cancer (Adem 2003, Thomassen 2008, Muendlein 2015, Wong-Brown 2015, Dudley 2018). BRCA1 c.4986+3G>C was not observed in large population cohorts (Lek 2016). The guanine (G) nucleotide that is altered is not conserved. Based on currently available evidence, we consider BRCA1 c.4986+3G>C to be a likely pathogenic variant. -

Jan 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

BRCA1: PP1:Strong, PM2, PS4:Moderate, PP3, PS3:Supporting -

Jan 01, 2020

GeneKor MSA

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant occurs three bases after exon 15 of the BRCA1 gene. Experimental studies have shown that this variant causes aberrant splicing in vitro, resulting in an out-of-frame insertion predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay (PMID: 23239986). This variant has been observed in multiple individuals with a personal and/or family history of breast and/or ovarian cancer (PMID: 23239986, 12491499). This variant is also known as BRCA1 IVS16+3G>C and 5105G>C using alternate nomenclature. The mutation database ClinVar contains several entries for this variant (Variation ID: 55341). -

Hereditary breast ovarian cancer syndrome Pathogenic:5

Jul 25, 2021

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.4986+3G>C alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Three predict the variant abolishes a 5 splicing donor site. At least one publication reports experimental evidence that this variant affects mRNA splicing (Wappenschmidt_2012). The variant was absent in 249776 control chromosomes (gnomAD). c.4986+3G>C has been reported in the literature in multiple individuals affected with breast and ovarian cancers (example: Rebbeck_2018, Wappenschmidt_2012). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence suggesting a loss on protein function (Findlay_2018). 12 ClinVar submitters (evaluation after 2014) cite the variant as likely pathogenic/pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Nov 13, 2023

Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Oct 10, 2024

German Consortium for Hereditary Breast and Ovarian Cancer, University Hospital Cologne

Significance: Likely pathogenic, low penetrance

Review Status: no assertion criteria provided

Collection Method: curation

Taking into accout the results of the splice analysis and the low LRs from segregation analysis we assume that this variant is likely to be a variant with reduced penetrance in comparision with other LOF-variants in BRCA1; According to the ClinGen ENIGMA BRCA1 v1.1.0 criteria we chose these criteria: PS1 (medium pathogenic): Apply PS1_Moderate, for exonic and intronic variants with same predicted impact on splicing, as a previously classified (likely) pathogenic variant. Vary weight depending on relative positions, and confidence in classification of the reference variant. Various variants in this splice site are classified as pathogenic e.g. c.4986+6T>G; +1/2, PS3 (strong pathogenic): Findlay et al. (PS3 met as per ENIGMA/ClinGen table 9), PM2 (supporting pathogenic): not in gnomAD (90 families in GC-HBOC), PP3 (supporting pathogenic): Variant is predicted to have a splice effect by SpliceAI (threshold: 0.2, value: 0.93). -

Dec 17, 2015

Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

Dec 13, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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 altered protein product. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with breast and/or ovarian cancer (PMID: 12491499, 18465347, 23239986, 23772696, 25682074, 25971625, 29446198). This variant is also known as IVS16+3G>C. ClinVar contains an entry for this variant (Variation ID: 55341). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in activation of a cryptic splice acceptor, and produces a non-functional protein and/or introduces a premature termination codon (PMID: 23239986, 31843900). For these reasons, this variant has been classified as Pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:2

Jan 10, 2023

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.4986+3G>C intronic pathogenic mutation results from a G to C substitution 3 nucleotides after coding exon 14 in the BRCA1 gene. This alteration has been detected in several breast and/or ovarian cancer families as well as in a patient with triple negative breast cancer (Adem C et al. Cancer 2003 Jan; 97(1):1-11; Thomassen M et al. Acta Oncol. 2008;47(4):772-7; Singer CF et al. Clin Genet. 2014 Jan;85(1):72-5; Wong-Brown MW et al. Breast Cancer Res Treat. 2015 Feb;150(1):71-80; Rebbeck TR et al. Hum. Mutat., 2018 May;39:593-620; Dudley B et al. Cancer, 2018 04;124:1691-1700; Carter NJ et al. Gynecol Oncol, 2018 12;151:481-488). One 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;562:217-222). In silico splice site analysis predicts that this alteration will weaken the native splice donor site. RT-PCR analysis of c.4986+3G>C revealed an alternate transcript with retention of 65 intronic nucleotides resulting in a premature termination codon (Ambry internal data; Wappenschmidt B et al. PLoS ONE 2012; 7(12):e50800). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Of note, this alteration is also designated as IVS16+3G>C in published literature. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

May 07, 2024

Color Diagnostics, LLC DBA Color Health

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant causes a G>C nucleotide substitution at the +3 position of intron 15 of the BRCA1 gene. RNA studies have observed aberrant splicing in carrier RNA that is expected to result in an absent or non-functional protein product (PMID: 23239986, 31843900). A functional study has reported that this variant impacts BRCA1 function in a haploid cell proliferation assay (PMID: 30209399). This variant has been detected in at least five individuals affected with breast, ovarian and pancreatic cancer (PMID: 12491499, 25682074, 25971625, 29360161, 35409996) and in suspected hereditary breast and ovarian cancer families (PMID: 18465347, 23772696). However, a multifactorial analysis has reported contradictory low segregation likelihood ratio for pathogenicity (LR) of 0.0001 and high tumor pathology LR of 418.5086 for this variant (PMID: 31131967). 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 Likely Pathogenic. -

BRCA1-related cancer predisposition Pathogenic:1

Apr 02, 2024

All of Us Research Program, National Institutes of Health

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The variant c.4986+3G>C in the BRCA1 gene is located in intron 15 and is predicted to result in aberrant splicing and a disrupted or absent protein product (SpliceAI donor loss score 0.93). This variant (also known as IVS16+3G>C) has been observed in multiple individuals with breast cancer, triple negative breast cancer, ovarian cancer, pancreatic cancer, or suspected breast and ovarian cancer (PMID: 12491499, 18465347, 23239986, 23772696, 25682074, 25971625, 29360161, 29446198, 30322717). Experimental studies have shown that this variant results in retention of 65 intronic nucleotides and leads to the protein change p.Met1663Valfs*14 (PMID: 23239986). Functional studies have also shown this variant to result in loss of function with impact on haploid cell survival (PMID: 30209399). This variant is absent in the general population database, gnomAD. Truncating variants in BRCA1 gene are known to be pathogenic (PMID: 21989022, 17661172, 22762150). Therefore, this variant is classified as pathogenic. -

Malignant tumor of breast Pathogenic:1

-

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

The BRCA1 c.4986+3G>C variant was identified in 3 of 1748 proband chromosomes (frequency: 0.002) from individuals or families with breast and ovarian cancer (Muendlein 2015, Wong-Brown 2015). The variant was also identified in dbSNP (ID: rs80358023) as “With Pathogenic allele”, Clinvitae database (as uncertain significance by ClinVar and Invitae, as Pathogenic by ClinVar), ARUP Laboratories BRCA Mutations Database (as definitely pathogenic), the ClinVar database (as uncertain significance by Invitae, Ambry Genetics; as likely pathogenic by GeneDx; as pathogenic by Counsyl and BIC), the BIC database (11X with clinical importance).rnThe c.4986+3G>C variant is located in the 5' splice region but does not affect the invariant +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 addition, 4 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing. In addition, the variant was found in triple-negative patient in preclinical study by Wong-Brown (2015). The study suggests the variant leads to intronic retention of 65 bp and creates premature stop codon at position 1663 (p.Met1663ValfsX14) and classified it as likely pathogenic. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more pathogenic role for this variant. This variant is classified as likely pathogenic. -

Hereditary breast ovarian cancer syndrome;C2676676:Breast-ovarian cancer, familial, susceptibility to, 1 Pathogenic:1

Sep 01, 2019

King Laboratory, University of Washington

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	7.4
DANN	Benign	0.72
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Mutation Taster		=0/100	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	0.99
dbscSNV1_RF	Pathogenic	0.77
Splicevardb		3.0
SpliceAI score (max)		0.93		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.93		Position offset: 3

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

Publications

LitVar

Other links and lift over

dbSNP: rs80358023; hg19: chr17-41222942;