rs80358158

Positions:

• chr17-43106534-C-A
• chr17-43106534-C-G
• chr17-43106534-C-T

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PVS1 PP4_Strong PS3

This summary comes from the ClinGen Evidence Repository: The c.135-1G>T variant is an intronic variant within the native acceptor 1,2 splice site occurring in intron 3 of the BRCA1 gene. This variant is present in gnomAD v2.1 (exomes only, non-cancer subset) or gnomAD v3.1 (non-cancer subset) but is below the ENIGMA BRCA1/2 VCEP threshold >0.00002 for BS1_Supporting (PM2_Supporting, BS1, and BA1 are not met). This variant is reported to result in aberrant mRNA splicing. RNAseq demonstrated that the variant impacts splicing by resulting in skipping of exon 4 from the transcript (PMID:30101128). Appropriate code strength determined by comparison of results to PVS1 decision tree (PVS1 (RNA) met). Reported by one calibrated study to exhibit protein function similar to pathogenic control variants (PMID:30209399) (PS3 met). Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 234999878.51 (based on Cosegregation LR=9528; Pathology LR=2.009; Family History LR=12277.7), above the threshold for Very strong evidence towards pathogenicity (LR >350) (PP4_Very strong met; PMID:31131967, 31853058).In summary, this variant meets the criteria to be classified as a Pathogenic variant for BRCA1-related cancer predisposition based on the ACMG/AMP criteria applied as specified by the ENIGMA BRCA1/2 VCEP (PVS1 (RNA), PS3, PP4_Very strong). LINK:https://erepo.genome.network/evrepo/ui/classification/CA000895/MONDO:0011450/092

• Frequency:
  • Genomes: 𝑓 0.000013 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0000035 (0 hom.)
• Consequence: BRCA1 NM_007294.4 splice_acceptor
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic reviewed by expert panel P:17 O:2
• Conservation: PhyloP100: 4.27

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 16 ACMG points.

• PVS1: For more information check the summary or visit ClinGen Evidence Repository.
• PS3: For more information check the summary or visit ClinGen Evidence Repository.
• PP4: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRCA1	NM_007294.4	c.135-1G>T		splice_acceptor_variant		ENST00000357654.9	NP_009225.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BRCA1	ENST00000357654.9	c.135-1G>T		splice_acceptor_variant		1	NM_007294.4	ENSP00000350283	P4

Frequencies

GnomAD3 genomes AF: 0.0000132 AC: 2 AN: 152032 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000294

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.00000402 AC: 1 AN: 248910 Hom.: 0 AF XY: 0.00000741 AC XY: 1 AN XY: 134914

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: 0.00000888

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000349 AC: 5 AN: 1431222 Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0 AN XY: 713600

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: 0.00000461

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0000132 AC: 2 AN: 152032 Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1 AN XY: 74260

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000294

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000708 Hom.: 0

ExAC AF: 0.00000824 AC: 1

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:4 Other:2

Pathogenic, no assertion criteria provided	clinical testing	Sharing Clinical Reports Project (SCRP)	May 21, 2012	- -
not provided, no classification provided	in vitro	Brotman Baty Institute, University of Washington	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Counsyl	Nov 12, 2015	- -
not provided, no classification provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA1)	-	- -
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, criteria provided, single submitter	clinical testing	Baylor Genetics	Mar 24, 2024	- -

Hereditary breast ovarian cancer syndrome Pathogenic:5

Pathogenic, criteria provided, single submitter	clinical testing	National Health Laboratory Service, Universitas Academic Hospital and University of the Free State	Nov 16, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	May 20, 2016	Variant summary: The BRCA1 c.135-1G>T variant involves the alteration of a conserved intronic nucleotide located at a canonical splice site. Mutation taster predicts a damaging outcome for this variant along with 5/5 in silico splice site prediction algorithms predicting the loss of the splice acceptor site. These predictions were confirmed by Tesoriero_HM_2005 which demonstrated the variant to result in exon skipping that creates an in-frame deletion of 26 amino acids from exon 5. The variant was found in 1/111484 control chromosomes at a frequency of 0.000009, which does not exceed the estimated maximal expected allele frequency of a pathogenic BRCA1 variant (0.0010005). It was reported in several HBOC patients and in at least one HBOC family it co-segregated with the disease (Tesoriero_HM_2005). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as Pathogenic. Taken together, this variant is classified as a Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 30, 2024	This sequence change affects an acceptor splice site in intron 3 of the BRCA1 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and likely results in a shortened protein product. This variant is present in population databases (rs80358158, gnomAD 0.002%). Disruption of this splice site has been observed in individual(s) with a personal or family history breast cancer (PMID: 9333265, 11179017, 16211554, 18445692, 20020529, 26187060). This variant is also known as IVS4-1G>T and IVS3-1G>T. ClinVar contains an entry for this variant (Variation ID: 37404). Based on a multifactorial likelihood algorithm using genetic, in silico, and/or statistical data, this variant has been determined to have a high probability of being pathogenic (PMID: 20020529). Studies have shown that disruption of this splice site results in skipping of exon 4, but is expected to preserve the integrity of the reading-frame (PMID: 16211554, 24212087; Invitae). This variant disrupts the p.Cys64 amino acid residue in BRCA1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 7894491, 11320250, 15131401, 23867111, 24516540, 26246475, 27257965, 29446198). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -
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	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jan 17, 2019	The c.135-1G>T variant in BRCA1 has been reported in more than 30 individuals with BRCA1-associated cancers and segregated with breast cancer in 10 relatives from 1 family (Shattuck-Eidens 1997, Risch 2001, Tesoriero 2005, Willems 2008, Rashid 2016, Breast Cancer Information Core (BIC)). This variant has been identified in 2/128060 European chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs80358158). This variant occurs in the invariant region (+/- 1,2) of the splice consensus sequence and functional studies have shown it results in an in-frame deletion of 26 amino acids(Tesoriero 2005, Wappenschmidt 2012). In summary, this variant meets criteria to be classified as pathogenic for HBOC in an autosomal dominant manner. ACMG/AMP criteria applied: PS4, PP1_Strong, PM2, PM4. -

not provided Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Nov 17, 2020	This variant is located in a canonical splice-acceptor site and interferes with normal BRCA1 mRNA splicing. In the published literature, this variant has been reported in multiple individuals with breast and/or ovarian cancer and shown to cause an in-frame deletion of exon 5 of the BRCA1 gene from experimental studies (PMID: 31131967 (2019), 30209399 (2018), 26187060 (2015), 25452441 (2015), 24212087 (2014), 21324516 (2011), 20020529 (2010), 18824701 (2008), 16211554 (2005), 9333265 (1997)). Based on the available information, this variant is classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Feb 27, 2024	Canonical splice site variant demonstrated to result in an in-frame loss of the adjacent exon, which is located in the critical RING finger domain, in a gene for which loss of function is a known mechanism of disease (PMID: 16211554, 8944023, 20104584, 23239986, 24389207); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; Not observed at significant frequency in large population cohorts (gnomAD); Also known as 254-1G>T, IVS4-1G>T; This variant is associated with the following publications: (PMID: 9333265, 21285146, 21324516, 27553291, 16683254, 28888541, 20020529, 11179017, 25525159, 18445692, 24212087, 16998791, 26187060, 21965345, 21769658, 16528604, 23239986, 30209399, 29446198, 29625052, 26689913, 30787465, 35464868, 29922827, 20104584, 24389207, 8944023, 30720243, 31131967, 32885271, 18824701, 30101128, 36451132, 34887416, 25452441, 16211554) -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Jan 30, 2023	- -

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Apr 26, 2021	This variant causes a G to T nucleotide substitution at the -1 position of intron 3 of the BRCA1 gene. RNA studies have shown that this variant impacts the splicing of exon 4 that partially encodes the RING domain, which is important for BRCA1 function and is noted to have clinically relevant mutations (PMID: 16211554, 22737296, 30101128). A functional study has shown that this variant impacts BRCA1 function in a haploid human cell proliferation assay (PMID: 30209399). This variant has been reported in at least 7 individuals affected with breast and ovarian cancer (PMID: 11179017, 16211554, 21324516, 25452441, 33471991; Leiden Open Variation Database DB-ID BRCA1_000503) and an individual affected with prostate cancer with a family history of breast cancer (PMID: 18445692). This variant also has been reported with a co-segregation likelihood ratio for pathogenicity of 9528 in one pedigree (PMID: 31131967). This variant has been identified in 2/280296 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. -
Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Dec 27, 2022	The c.135-1G>T intronic pathogenic mutation results from a G to T substitution one nucleotide upstream from coding exon 3 of the BRCA1 gene. This mutation has been identified in multiple breast, ovarian and/or prostate cancer families (Zhang S et al. Gynecol. Oncol. 2011 May;121(2):353-7; Rashid MU et al. Int. J. Cancer 2006 Dec;119(12):2832-9; Tesoriero AA et al. Hum. Mutat. 2005 Nov;26(5):495. Risch HA et al. Am. J. Hum. Genet. 2001 Mar;68(3):700-10. Shattuck-Eidens D et al. JAMA 1997 Oct;278(15):1242-50; Willems AJ et al. Clin. Cancer Res. 2008; 14:2953-61). This variant gives rise to an in -frame deletion of coding exon 3 (also known as exon 5 in the literature-Tesoriero AA et al. Hum Mutat. 2005 Nov;26(5):495; Farber-Katz S et al. Front Oncol, 2018 Jul;8:286). One functional study found that this nucleotide substitution is non-functional in a high throughput genome editing haploid cell survival assay (Findlay GM et al. Nature, 2018 10;562:217-222). Of note, this alteration is also designated as IVS3-1G>T and IVS4-1G>T in the published literature. In addition to the clinical data presented in the literature, alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as a disease-causing mutation. -

BRCA1-related cancer predisposition Pathogenic:1

Pathogenic, reviewed by expert panel

curation

ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen

Jun 11, 2024

The c.135-1G>T variant is an intronic variant within the native acceptor 1,2 splice site occurring in intron 3 of the BRCA1 gene. This variant is present in gnomAD v2.1 (exomes only, non-cancer subset) or gnomAD v3.1 (non-cancer subset) but is below the ENIGMA BRCA1/2 VCEP threshold >0.00002 for BS1_Supporting (PM2_Supporting, BS1, and BA1 are not met). This variant is reported to result in aberrant mRNA splicing. RNAseq demonstrated that the variant impacts splicing by resulting in skipping of exon 4 from the transcript (PMID: 30101128). Appropriate code strength determined by comparison of results to PVS1 decision tree (PVS1 (RNA) met). Reported by one calibrated study to exhibit protein function similar to pathogenic control variants (PMID: 30209399) (PS3 met). Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 234999878.51 (based on Cosegregation LR=9528; Pathology LR=2.009; Family History LR=12277.7), above the threshold for Very strong evidence towards pathogenicity (LR >350) (PP4_Very strong met; PMID: 31131967, 31853058). In summary, this variant meets the criteria to be classified as a Pathogenic variant for BRCA1-related cancer predisposition based on the ACMG/AMP criteria applied as specified by the ENIGMA BRCA1/2 VCEP (PVS1 (RNA), PS3, PP4_Very strong). -

Familial cancer of breast;C2676676:Breast-ovarian cancer, familial, susceptibility to, 1;C3280442:Pancreatic cancer, susceptibility to, 4;C4554406:Fanconi anemia, complementation group S Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

May 13, 2022

- -

Malignant tumor of breast Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

-

The BRCA1 c.135-1G>T variant has been shown to give rise to an in-frame deletion of exon 5 (BRCA1 c.135_212del) that is predicted to encode 26 amino acids. One study used the multifactorial likelihood analysis and variant segregation in families by Bayes analysis to evaluate the clinical significance of this variant. The Bayes scores from a single family with BRCA1 c.135-1G>T was 9528:1, providing strong evidence of causality for this variant; in addition, inclusion of pathology features gave an overall likelihood of causality of 28108:1 (Spurdle_2010). The variant was identified in dbSNP (ID: rs80358158) as “With Pathogenic allele” and in the Clinvitae and Clinvar databases as pathogenic by Ambry Genetics; GeneDx; Quest Diagnostics Nichols Institute San Juan Capistrano; Consortium of Investigators of Modifiers of BRCA1/2, University of Cambridge and SCRP. The variant was further identified in ARUP Laboratories BRCA Mutations Database as definitely pathogenic and in the Fanconi Anemia Mutation Database (LOVD), which refer to the multifactorial likelihood score of 28108:1. The variant was not identified in the COSMIC, GeneInsight COGR, UMD, and the BIC databases. In addition, the variant was identified in the the Exome Aggregation Consortium database (August 8th 2016) in 1 of 111484 chromosomes (freq. 0.000009) in the European (Non-Finnish) population but not seen in the African, East Asian, European (Finnish), Latino and South Asian populations. The variant was not identified in the 1000 Genomes Project, the NHLBI GO Exome Sequencing Project, and the genome Aggregation Database (beta, October 19th 2016. The c.135-1G>T variant is predicted to cause abnormal splicing because the nucleotide substitution occurs in the invariant region of the splice consensus sequence. 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. In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.39	D
BayesDel_noAF	Pathogenic	0.32
CADD	Pathogenic	29
DANN	Uncertain	0.99
Eigen	Pathogenic	1.0
Eigen_PC	Pathogenic	0.85
FATHMM_MKL	Uncertain	0.94	D
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D
GERP RS		4.6

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.93
SpliceAI score (max)		0.86		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.86		Position offset: -1

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

Publications

LitVar

Other links and lift over

dbSNP: rs80358158; hg19: chr17-41258551; COSMIC: COSV100524937; COSMIC: COSV100524937;