17-43070924-T-A

Variant names:

• chr17-43070924-T-A
• rs80358087
• NM_007294.4:c.4986+4A>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+4A>T variant causes a splice 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. 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: 6.8e-7 (0 hom.)
• Consequence: BRCA1 NM_007294.4 splice_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 11 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: Multiple lines of computational evidence support a deleterious effect 4: Cadd, dbscSNV1_ADA, dbscSNV1_RF, max_spliceai [when BayesDel_noAF, Dann was below the threshold]
• 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 rank	MANE	Protein	UniProt
BRCA1	NM_007294.4	c.4986+4A>T		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+4A>T		splice_region_variant, intron_variant	Intron 15 of 22	1	NM_007294.4	ENSP00000350283.3

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

May 11, 2016

Counsyl

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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

- -

Jul 01, 2023

Baylor Genetics

Significance: 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

- -

Oct 09, 2012

Sharing Clinical Reports Project (SCRP)

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

- -

not provided Pathogenic:4

Aug 01, 2024

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The BRCA1 c.4986+4A>T variant has been reported in the published literature in individuals and families with hereditary breast and or ovarian cancer syndrome (PMID: 16267036 (2005), 21203900 (2011)). A large-scale study using a haploid cell line showed that this variant apparently lost functional activity (PMID: 30209399 (2018)). In addition, this variant was observed to result in abnormal splicing (personal communication with Ambry Genetics related to ClinVar ID: 55342). Also, other variants at the same nucleotide position (c.4986+4A>G) and adjacent intronic variants show altered splicing resulting in a truncated protein (PMID: 10406662 (1999), 16619214 (2006), 23239986 (2012), 23451180 (2013)). This variant has not been reported in large, multi-ethnic general populations (Genome Aggregation Database, http://gnomad.broadinstitute.org). Analysis of this variant using software algorithms for the prediction of the effect of nucleotide changes on splicing yielded predictions that this variant may affect proper BRCA1 mRNA splicing. Based on the available information, this variant is classified as likely pathogenic. -

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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+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. -

Jan 10, 2022

GeneDx

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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) -

Jan 01, 2020

GeneKor MSA

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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). -

Hereditary cancer-predisposing syndrome Pathogenic:2

Jan 03, 2020

Color Diagnostics, LLC DBA Color Health

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

Mar 25, 2024

Ambry Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

Hereditary breast ovarian cancer syndrome Pathogenic:2

Jan 27, 2025

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. 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 gene product 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. -

Aug 30, 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+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. -

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;