rs80358087

Positions:

• chr17-43070924-T-A
• chr17-43070924-T-C
• chr17-43070924-T-G

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM2 PP3_Moderate PP5_Very_Strong

The NM_007294.4(BRCA1):​c.4986+4A>T variant causes a splice donor region, intron change. The variant allele was found at a frequency of 0.000000684 in 1,461,770 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: BRCA1 NM_007294.4 splice_donor_region, intron
• Scores: Splicing: ADA: 0.9999
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:13 O:1
• Conservation: PhyloP100: 4.31

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 12 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 17-43070924-T-A is Pathogenic according to our data. Variant chr17-43070924-T-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 55342.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-43070924-T-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRCA1	NM_007294.4	c.4986+4A>T		splice_donor_region_variant, intron_variant		ENST00000357654.9	NP_009225.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BRCA1	ENST00000357654.9	c.4986+4A>T		splice_donor_region_variant, intron_variant		1	NM_007294.4	ENSP00000350283	P4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461770 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 727214

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 8.99e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:13 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

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

Pathogenic, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA1)	May 29, 2002	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Counsyl	May 11, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Jul 01, 2023	- -
Pathogenic, no assertion criteria provided	clinical testing	Sharing Clinical Reports Project (SCRP)	Oct 09, 2012	- -
Pathogenic, criteria provided, single submitter	clinical testing	Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge	Oct 02, 2015	- -
not provided, no classification provided	in vitro	Brotman Baty Institute, University of Washington	-	- -

not provided Pathogenic:4

Likely pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Sep 07, 2018	Not found in the total gnomAD dataset, and the data is high quality (0/275154 chr). Found in at least one symptomatic patient. Predicted to negatively affect a known splice site. Nucleotide conservation is uninformative. Assessment of experimental evidence suggests this variant results in abnormal protein function. -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jan 10, 2022	Published functional studies demonstrate a damaging effect: classified as non-functional based on a saturation genome editing (SGE) assay measuring cell growth (Findlay 2018); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on splicing; Observed in individuals with hereditary breast/ovarian cancer (Judkins 2005, Konecny 2011, Rebbeck 2018); Also known as 5105+4A>T; This variant is associated with the following publications: (PMID: 29446198, 21203900, 23239986, 23348723, 16267036, 30209399, 31360904, 30787465) -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneKor MSA	Jan 01, 2020	This sequence change occurs 4 bases after exon 15 of the BRCA1 gene. This position is conserved in the human and other genomes and might be involved in mRNA processing. This variant is expected to result in incorrect splicing, alteration in the reading frame and an absent or truncated protein. This variant is also known as 5105+4A>T and has been described in the literature in at least two families with hereditary breast and ovarian cancer (PMID: 21203900). This sequence change is listed in population databases at very low frequency (rs80358087, <0.1%). The mutation database ClinVar contains entries for this variant (Variation ID: 55342). -
Likely pathogenic, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The BRCA1 c.4986+4A>T variant was identified in 9 of 112430 proband chromosomes (frequency: 0.0001) from individuals or families with breast or ovarian cancer (Judkins 2005, Konecny 2011). The variant was also identified in dbSNP (ID: rs80358087) as "With Likely pathogenic, Pathogenic allele", in ClinVar (classified as likely benign by GeneDx, Counsyl, Ambry Genetics, Invitae, GeneKor MSA; as pathogenic by CIMBA, Integrated Genetics/Laboratory Corporation of America, SCRP, BIC), LOVD 3.0 (4x conflicting interpretations of pathogeny), BIC Database (3x with clinical importance), and ARUP Laboratories (class 5 - definitely pathogenic), databases. The variant was not identified in GeneInsight-COGR, UMD-LSDB, or in the Zhejiang University Database. The variant was not identified in the following control databases: the 1000 Genomes Project, the NHLBI GO Exome Sequencing Project, or the Genome Aggregation Database (Feb 27, 2017). The c.4986+4A>T 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, 5 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing. Several studies identified different nucleotides change at the same nucleotide position (c.4986+4A>G and c.4986+4A>C) (Wappenschmidt 2012, Meisel 2014). The c.4986+4A>G alteration create an aberrant transcript, which incorporates 65 intronic sequences following exon 16, and creates a stop codon at 1676 (p.Met1663ValfsX14) (Wappenschmidt 2012), which may be crucial for normal RNA splicing. 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 cancer-predisposing syndrome Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Mar 25, 2024	The c.4986+4A>T intronic variant results from an A to T substitution 4 nucleotides after coding exon 14 in the BRCA1 gene. This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. RNA studies for this alteration and a close match alteration, c.4986+4A>G, demonstrate retention of 65 nucleotides of the following intron leading to a frameshift and predicted premature termination codon (Ambry internal data; Wappenschmidt B et al. PLoS ONE, 2012 Dec;7:e50800). This same work and others show the same aberrant transcript results from other nucleotide substitutions at this splice site from the c.4986+1 through the c.4986+6 positions (Scholl T et al. Am. J. Med. Genet., 1999 Jul;85:113-6; Chen X et al. Hum. Mutat., 2006 May;27:427-35; Vreeswijk MP et al. Hum. Mutat., 2009 Jan;30:107-14; Wappenschmidt B et al. PLoS ONE, 2012 Dec;7:e50800; Colombo M et al. PLoS ONE, 2013 Feb;8:e57173). These alterations have also been observed in breast and ovarian cancer cohorts and some have been observed to segregate with disease in these families (Konecny M et al. Breast Cancer Res. Treat., 2011 Feb;126:119-30; Rebbeck TR et al, Hum Mutat, 2018 05;39:593-620; Ambry internal data). In addition, this variant, as well as the variants described as close matches, were non-functional in a high throughput genome editing haploid cell survival assay (Findlay GM et al. Nature, 2018 10;562:217-222). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the majority of available evidence to date, this variant is likely to be pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jan 03, 2020	This variant causes an A>T nucleotide substitution at the +4 position of intron 15 of the BRCA1 gene. Splice site prediction tools predict that this variant may have a significant impact on RNA splicing. Another variant at this position results in the use of a cryptic donor at +65 nt and p.Met1663Valfs*14 as determined by RT-PCR of carrier RNA (PMID 23239986). This variant has been reported to be loss-of-function in a haploid cell proliferation assay (PMID: 30209399). This variant has been reported in two suspected hereditary breast/ovarian cancer families (PMID: 30209399). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic. -

Hereditary breast ovarian cancer syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Aug 30, 2021	Variant summary: BRCA1 c.4986+4A>T 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, while one predict the variant weakens a 5' donor site. An in vitro study that assessed the effect of the variant in a haploid human cell line whose survival is dependent on intact BRCA1 function, found that the variant resulted in loss of function (Findlay_2018). In addition, the variant is located in close proximity to other known pathogenic variants, such IVS16+3G>C, IVS16+4A>C, IVS16+6T>G, IVS16+6T>C that were proven to impair the splice donor site of intron 16 and showed incorporation of 65 nucleotide of the 5' end of intron 16 in all cases (Wappenschmidt_2012). The variant was absent in 249776 control chromosomes (gnomAD). c.4986+4A>T has been reported in the literature in individuals affected with Hereditary Breast and Ovarian Cancer (Konency_2011, Judkins_2005, Rebbeck_2018). These data indicate that the variant is likely to be associated with disease. Eight clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Oct 06, 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. It affects a nucleotide within the consensus splice site. 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: 21203900). ClinVar contains an entry for this variant (Variation ID: 55342). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this variant affects BRCA1 function (PMID: 30209399). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant disrupts the c.4986+4A nucleotide in the BRCA1 gene. Other variant(s) that disrupt this nucleotide have been determined to be pathogenic (PMID: 23239986, 25281711, 29446198, 30209399). 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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Pathogenic	29
DANN	Benign	0.93
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.89
SpliceAI score (max)		0.81		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.69		Position offset: 2
DS_DL_spliceai		0.81		Position offset: 4

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

Publications

LitVar

Other links and lift over

dbSNP: rs80358087; hg19: chr17-41222941;