17-43104262-C-T

Variant names:

• chr17-43104262-C-T
• rs80358116
• NM_007294.4:c.302-1G>A

Variant summary

Our verdict is Pathogenic. The variant received 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_007294.4(BRCA1):​c.302-1G>A variant causes a splice acceptor, intron change. The variant allele was found at a frequency of 0.000000687 in 1,456,556 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Likely pathogenic (★★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: BRCA1 NM_007294.4 splice_acceptor, intron
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:12
• Conservation: PhyloP100: 4.25
• Publications: 19 publications found

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]

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
• Fanconi anemia, complementation group S

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae), ClinGen, Ambry Genetics
• pancreatic cancer, susceptibility to, 4

  Inheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
• hereditary breast ovarian cancer syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• Fanconi anemia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Pathogenic. The variant received 18 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) 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
• PP5: Variant 17-43104262-C-T is Pathogenic according to our data. Variant chr17-43104262-C-T is described in ClinVar as Pathogenic/Likely_pathogenic. ClinVar VariationId is 54750.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.302-1G>A		splice_acceptor intron	N/A	NP_009225.1
	BRCA1	NM_001407581.1		c.302-1G>A		splice_acceptor intron	N/A	NP_001394510.1
	BRCA1	NM_001407582.1		c.302-1G>A		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.302-1G>A		splice_acceptor intron	N/A	ENSP00000350283.3
	BRCA1	ENST00000471181.7	TSL:1	c.302-1G>A		splice_acceptor intron	N/A	ENSP00000418960.2
	BRCA1	ENST00000470026.6	TSL:1	c.302-1G>A		splice_acceptor intron	N/A	ENSP00000419274.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.87e-7 AC: 1 AN: 1456556 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 724900

African (AFR) AF: 0.0000300 AC: 1 AN: 33360

American (AMR) AF: 0.00 AC: 0 AN: 44638

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26112

East Asian (EAS) AF: 0.00 AC: 0 AN: 39620

South Asian (SAS) AF: 0.00 AC: 0 AN: 85908

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53224

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5752

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1107718

Other (OTH) AF: 0.00 AC: 0 AN: 60224

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:12

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 1 Pathogenic:5

Feb 20, 2004

Breast Cancer Information Core (BIC) (BRCA1)

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

May 03, 2020

Genomic Research Center, Shahid Beheshti University of Medical Sciences

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Sep 26, 2022

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Nov 08, 2023

All of Us Research Program, National Institutes of Health

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.302-1G>A variant of the BRCA1 gene is predicted to affect mRNA splicing resulting in an absent or disrupted protein product. RT-PCR studies showed that the change resulted in a 10-base frameshift deletion from the beginning of coding exon 5 (exon 7 in the literature, PMID: 18712473). This variant has been reported in unrelated individuals with breast cancer (PMID: 18712473, 29907814, 33558524). This variant has not been identified in the general population (gnomAD). Loss-of-function variants in BRCA1 are known to be pathogenic (PMID: 21989022, 17661172, 22762150). Therefore, the c.302-1G>A variant of BRCA1 is classified as pathogenic.

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

not provided Pathogenic:2

Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

Hereditary cancer-predisposing syndrome Pathogenic:2

Mar 20, 2024

Ambry Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.302-1G>A intronic variant results from a G to A substitution one nucleotide upstream from coding exon 5 of the BRCA1 gene. This alteration, also referred to as IVS6-1G>A in the published literature, has been reported in multiple hereditary breast and/or ovarian cancer (HBOC) families (Osorio A et al. Eur J Hum Genet, 2003 Jun;11:489-92; Rebbeck TR et al. Hum Mutat, 2018 05;39:593-620; Palmero EI et al. Sci Rep, 2018 06;8:9188). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site and will result in the creation or strengthening of a novel splice acceptor site. In addition to the clinical data presented in the literature, RNA assays have demonstrated that this alteration results in aberrant splicing of a 10 nucleotide deletion from the beginning of coding exon 5 (exon 7 in the literature), which results in an mRNA transcript that is subject to nonsense-mediated decay (Ambry internal data; Gutiérrez-Enríquez S et al. Breast Cancer Res Treat 2009 Sep;117(2):461-5; Montalban G et al. Hum Mutat 2019 12;40(12):2296-2317). Based on the majority of available evidence to date, this variant is likely to be pathogenic.

Feb 20, 2023

Color Diagnostics, LLC DBA Color Health

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant causes a G to A nucleotide substitution at the -1 position of intron 5 splice acceptor site of the BRCA1 gene. This variant is also known as IVS6-1G>A by the BIC nomenclature. Two RNA studies have shown that this variant weakens the native splice acceptor and activates a cryptic acceptor 10-base downstream, resulting in r.302_311del (p.Tyr101Serfs*15) and a premature protein truncation (PMID: 18712473, 31343793). Quantitative PCR and allelic imbalance analyses on carrier RNA showed that the variant pre-mRNA does not produce a full-length mRNA transcript (PMID: 30472649, 31343793). This variant has been reported in an individual affected with bilateral breast cancer with breast cancer in a first-degree relative (PMID: 18712473), an individual with early onset breast cancer (PMID: 33558524), and in at least five additional individuals affected with hereditary breast and ovarian cancer (PMID: 30472649, 31343793; Ramon et al., 2020, DOI: 10.1200/JCO.2020.38.15_suppl.e13645). 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:2

Mar 14, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change affects an acceptor splice site in intron 5 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. This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with breast cancer (PMID: 18712473). This variant is also known as IVS6-1G>A. ClinVar contains an entry for this variant (Variation ID: 54750). Studies have shown that disruption of this splice site alters BRCA1 gene expression (PMID: 31343793). Studies have shown that disruption of this splice site results in activation of a cryptic splice site and introduces a premature termination codon (PMID: 18712473, 31343793). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic.

Mar 01, 2019

Hereditary Cancer Genetics group, Vall d'Hebron Institute of Oncology

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: research

Malignant tumor of breast Pathogenic:1

Apr 08, 2020

Center of Medical Genetics and Primary Health Care

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: research

ACMG Guidelines 2015 criteria The BRCA1 intronic/splice site variant c.302-1G>A is just before exon 7 sequence coding for Y101-147L aa. The closest functional domain is BRCA1, serine-rich domain (A344-507R). This splice site variant could result in a truncated or altered protein, potentially interfering with its function in DNA repair as an established disease mechanism in hereditary breast and ovarian cancer (PVS1 Pathogenic Very Strong). The variant is not found in GnomAD exomes neither in GnomAD genomes (PM2 Pathogenic Moderate). Several variants have been reported in this splice site either at position c.302-1 or c.302-2 (source, ClinVar). 4 pathogenic predictions from DANN, EIGEN, FATHMM-MKL and MutationTaster versus no benign predictions support its deleterious effect (PP3 Pathogenic Supporting). This variant was previously reported in ClinVar in patients diagnosed with Hereditary breast and ovarian cancer syndrome. In our study this variant was found in a 32-year-old female with unilateral breast cancer and no reported family history. Based on the available data, we classified this variant as a Pathogenic.

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.41	D
BayesDel_noAF	Pathogenic	0.35
CADD	Pathogenic	35
DANN	Uncertain	0.99
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	0.92
FATHMM_MKL	Uncertain	0.93	D
PhyloP100		4.2
GERP RS		5.3
Mutation Taster		=0/100	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.93
Splicevardb		3.0
SpliceAI score (max)		1.0		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.98		Position offset: -11
DS_AL_spliceai		1.0		Position offset: -1

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

Other links and lift over

dbSNP: rs80358116; hg19: chr17-41256279;