17-43057051-C-T

Variant names:

• chr17-43057051-C-T
• rs80358150
• NM_007294.4:c.5277+1G>A

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1_Moderate PM2 PP5_Very_Strong

The NM_007294.4(BRCA1):​c.5277+1G>A variant causes a splice donor, intron change. The variant allele was found at a frequency of 0.00000137 in 1,461,684 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 Pathogenic (★★★).

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: BRCA1 NM_007294.4 splice_donor, intron
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic reviewed by expert panel P:29 O:2
• Conservation: PhyloP100: 4.68

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.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.015021459 fraction of the gene. No cryptic splice site detected. Exon removal is inframe change.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 17-43057051-C-T is Pathogenic according to our data. Variant chr17-43057051-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 37654.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr17-43057051-C-T is described in Lovd as [Pathogenic]. Variant chr17-43057051-C-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRCA1	NM_007294.4	c.5277+1G>A		splice_donor_variant, intron_variant	Intron 19 of 22	ENST00000357654.9	NP_009225.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRCA1	ENST00000357654.9	c.5277+1G>A		splice_donor_variant, intron_variant	Intron 19 of 22	1	NM_007294.4	ENSP00000350283.3

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1461684 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 727156

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: 0.00000180

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 31

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:29 Other:2

Revision: reviewed by expert panel

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 1 Pathogenic:11 Other:1

Jul 19, 2023

All of Us Research Program, National Institutes of 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 19 of the BRCA1 gene. This variant is also known as IVS20+1G>A by a legacy nomenclature in the literature. RNA studies have found that this variant results in the retention of 87 nucleotides from intron 19 and the skipping of exon 19, that are predicted to cause in-frame insertion of 29 amino acids in the BRCT domain and out-of-frame splicing, respectively (PMID: 16211554, 24667779, 31843900). A functional study has reported that this variant impacts BRCA1 function in a haploid cell proliferation assay (PMID: 30209399). This variant has been reported in several individuals affected with breast or ovarian cancer, one individual affected with peritoneal cancer (PMID: 14574155, 16211554, 20215541, 21913181, 23096355) and in at least four dozen suspected hereditary breast and ovarian cancer families (PMID: 11149413, 11597388, 11802209, 16683254, 19949876, 24285858), including one family in which this variant segregates with ovarian cancer in five members of one family (PMID: 16211554). This variant also has been detected in a breast cancer case-control meta-analysis in 8/60466 cases and 1/53461 unaffected individuals (PMID: 33471991; Leiden Open Variation Database DB-ID BRCA1_000441). A multifactorial analysis has reported a family history likelihood ratio for pathogenicity of 11.1 (PMID: 17924331). 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. -

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

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Dec 30, 1999

Breast Cancer Information Core (BIC) (BRCA1)

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

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Aug 10, 2015

Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)

Significance: Pathogenic

Review Status: reviewed by expert panel

Collection Method: curation

IARC class based on posterior probability from multifactorial likelihood analysis, thresholds for class as per Plon et al. 2008 (PMID: 18951446). Class 5 based on posterior probability = 1 -

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Brotman Baty Institute, University of Washington

Significance: not provided

Review Status: no classification provided

Collection Method: in vitro

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Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

May 02, 2012

Sharing Clinical Reports Project (SCRP)

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Aug 19, 2014

Counsyl

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: literature only

- -

Sep 21, 2015

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 13, 2024

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Oct 08, 2014

Genome Diagnostics Laboratory, University Medical Center Utrecht

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Neuberg Centre For Genomic Medicine, NCGM

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The invariant splice donor c.5277+1G>A variant in BRCA1 gene has been reported previously in heterozygous state in multiple individuals affected with Hereditary Breast and/or Ovarian cancer Steffensen AY, et al., 2014; van Harssel JJ, et al., 2010; van der Hout AH, et al., 2006. This variant has been known to segregate with disease. Functional studies indicate that this variant leads to skipping of exon 20 and creates a premature stop codon, proving a damaging effect Tesoriero AA, et al., 2005. The c.5277+1G>A variant is novel not in any individuals in gnomAD Exomes and 1000 Genomes. This variant has been reported to the ClinVar database as Pathogenic multiple submissions. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Pathogenic. -

not provided Pathogenic:5 Other:1

Apr 12, 2024

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The BRCA1 c.5277+1G>A variant disrupts a canonical splice-donor site and interferes with normal BRCA1 mRNA splicing. This variant has been reported in the published literature in individuals affected with breast and/or ovarian cancer (PMIDs: 38439815 (2024), 36329109 (2022), 33471991 (2021), 23096355 (2012)). Functional evidence suggests that this variant may impact protein function and interfere with normal BRCA1 mRNA splicing (PMIDs: 38398132 (2024), 31843900 (2019), 24667779 (2014), 20215541 (2010), 16211554 (2005)). This variant has not been reported in large, multi-ethnic general populations (Genome Aggregation Database, http://gnomad.broadinstitute.org). Based on the available information, this variant is classified as pathogenic. -

Feb 20, 2019

Revvity Omics, Revvity

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Oct 25, 2021

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Canonical splice site variant demonstrated to result in an in-frame deletion of a critical region (Tesoriero 2005, Sanz 2010, Steffensen 2014); Multifactorial studies suggest this variant is associated with breast and ovarian cancer (Easton 2007, Lindor 2012); 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 in large population cohorts (Lek 2016); Deletions involving coding exons in this gene are frequently reported as pathogenic, regardless of frame prediction (Stenson 2014); Observed in individuals with early-onset or familial breast and/or ovarian cancer (de la Hoya 2001, Diez 2003, van Harssel 2010, Lara 2012); Classified as pathogenic by a well-established clinical consortium and/or database (ClinVar SCV000244394.1; Landrum 2016); Also known as 5396+1G>A or IVS20+1G>A; This variant is associated with the following publications: (PMID: 23348723, 23096355, 19593635, 20215541, 19949876, 18286383, 18528753, 25849179, 18298804, 26913838, 29446198, 17924331, 21990134, 25525159, 11149413, 12955716, 16211554, 25859162, 24667779, 28636540, 28477318, 28918466, 30209399, 30720863, 25085752, 32665702) -

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Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

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Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

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MutSpliceDB: a database of splice sites variants effects on splicing, NIH

Significance: not provided

Review Status: no classification provided

Collection Method: in vitro

- -

Hereditary cancer-predisposing syndrome Pathogenic:4

Oct 30, 2017

True Health Diagnostics

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Aug 05, 2022

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.5277+1G>A intronic pathogenic mutation results from a G to A substitution one nucleotide after coding exon 18 of the BRCA1 gene. This mutation has been identified in multiple breast and/or ovarian cancer families (de la Hoya M et al. Int. J. Cancer. 2001 Jan;91:137-40; Verhoog LC et al. Eur. J. Cancer. 2001 Nov;37:2082-90; Meindl A et al. Int. J. Cancer. 2002 Feb;97:472-80; Díez O et al Hum. Mutat. 2003 Oct;22:301-12; Piek JM et al. Fam. Cancer. 2003;2:73-8; Lara K et al. Biol. Res. 2012;45:117-30). This alteration has been classified as definitely pathogenic by multifactorial analysis, which integrates the following lines of evidence to produce a quantitative likelihood of pathogenicity: in silico prediction models, segregation with disease, tumor characteristics, and mutation co-occurrence (Easton DF et al. Am. J. Hum. Genet. 2007 Nov;81:873-83; Lindor NM et al. Hum. Mutat. 2012 Jan;33:8-21; Vallee MP et al. Hum. Mutat. 2012 Jan;33:22-8). Multiple RNA studies have demonstrated that this alteration results in abnormal splicing (Tesoriero AA et al. Hum. Mutat. 2005 Nov;26:495; Elstrodt F et al. Cancer Res. 2006 Jan;66:41-5; Steffensen AY et al. Eur. J. Hum. Genet. 2014 Dec;22:1362-8; Tesoriero AA et al. Hum. Mutat. 2014 Apr;35:511; Ambry internal data). 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). Of note, this mutation is also designated as IVS20+1G>A and 5396+1G>A in 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. -

Oct 02, 2024

Molecular Diagnostics Laboratory, Catalan Institute of Oncology

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PVS1, PS3, PM2_Supporting, PP4_VeryStrong c.5277+1G>A, located in a canonic splicing site of the BRCA1 is predicted to alter splicing causing the skipping of exon 19 (20, according to BIC nomenclature), and the retention of 87 nucleotides from intron 19 (r.[5194_5277del,5277_5278ins5277+1_5277+87]), which translates into p.[His1732_Lys1759del,Lys1759_Ile1760insValLysLeuProProSerSer*] (PMID: 24667779, 20215541, 16211554). This alteration, also known as IVS20+1G>A, generates two transcripts, one in-frame deletion affecting a (potentially) clinically important functional protein domain and another producing a loss of function by premature protein truncation and nonsense-mediated mRNA decay (PVS1_RNA). It is not present in the population database gnomAD v2.1.1, non cancer dataset (PM2_supporting). Reported by one calibrated study incorporating mRNA splicing effects to affect protein function similar to pathogenic control variants (PMID:30209399) (PS3). It has been reported in the literature in multiple individuals affected with Hereditary Breast and Ovarian Cancer Syndrome and other types of cancers, and the likelihood ratio reported by multifactorial analysis is 4.27E+11 (PP4_Very Strong). In addition, the variant has been identified in the ClinVar database (28x pathogenic), in the BRCA Exchange database (where it has been classified as pathogenic), and in LOVD (not classified). Based on currently available information, the variant c.5277+1G>A should be considered a pathogenic variant. -

May 10, 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 19 of the BRCA1 gene. This variant is also known as IVS20+1G>A by a legacy nomenclature in the literature. RNA studies have found that this variant results in the retention of 87 nucleotides from intron 19 and the skipping of exon 19, that are predicted to cause in-frame insertion of 29 amino acids in the BRCT domain and out-of-frame splicing, respectively (PMID: 16211554, 24667779, 31843900). A functional study has reported that this variant impacts BRCA1 function in a haploid cell proliferation assay (PMID: 30209399). This variant has been reported in several individuals affected with breast or ovarian cancer, one individual affected with peritoneal cancer (PMID: 14574155, 16211554, 20215541, 21913181, 23096355) and in at least four dozen suspected hereditary breast and ovarian cancer families (PMID: 11149413, 11597388, 11802209, 16683254, 19949876, 24285858), including one family in which this variant segregates with ovarian cancer in five members of one family (PMID: 16211554). This variant also has been detected in a breast cancer case-control meta-analysis in 8/60466 cases and 1/53461 unaffected individuals (PMID: 33471991; Leiden Open Variation Database DB-ID BRCA1_000441). A multifactorial analysis has reported a family history likelihood ratio for pathogenicity of 11.1 (PMID: 17924331). 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:4

Jan 31, 2014

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

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: research

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Feb 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.5277+1G>A is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes a 5' splicing donor site. These predictions have been confirmed by experimental evidence showing the variant to result in the skipping of exon 20 and generating a truncated protein (Tesoriero_2005). The variant was absent in 251494 control chromosomes. c.5277+1G>A has been reported in the literature in multiple individuals affected with Hereditary Breast And Ovarian Cancer Syndrome (eg Meindl_2002, Diez_2003, Tesoriero_2012, Lara_2012, Litton_2012, Brohet_2014, etc). 12 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. Based on the evidence outlined above, the variant was classified as pathogenic. -

Dec 30, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change affects a donor splice site in intron 19 of the BRCA1 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or altered 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 or ovarian cancer (PMID: 11149413, 16683254, 19949876). ClinVar contains an entry for this variant (Variation ID: 37654). 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: 17924331). Studies have shown that disruption of this splice site results in activation of a cryptic splice site in intron 19 or skipping of exon 19 (also known as exon 20) , and produces a non-functional protein and/or introduces a premature termination codon (PMID: 24667779; internal data). For these reasons, this variant has been classified as Pathogenic. -

Nov 01, 2021

Genetics Program, Instituto Nacional de Cancer

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

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not specified Pathogenic:1

May 24, 2017

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breast and/or ovarian cancer Pathogenic:1

Jan 22, 2016

Foulkes Cancer Genetics LDI, Lady Davis Institute for Medical Research

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

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

Apr 05, 2024

Fulgent Genetics, Fulgent Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Malignant tumor of breast Pathogenic:1

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Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

The c.5277+1G>A variant has been previously reported in the literature in at least 5 of 3526 proband chromosomes in individuals with hereditary breast and ovarian cancer (De La Hoya 2001, Sanz 2010, Diez 2003, Easton 2007, Tesoriero 2005). In one study, bilateral breast cancer was noted and the presence of other cancers in the family (Diez 2003). In two studies, disease status was noted in 6 individuals (1 with breast and 5 with ovarian) and the variant was shown to segregate with disease in at least one affected family member (Sanz 2010, Tesoriero 2005). Tesoriero et al. (2005) carried out functional studies and determined that this variant leads to two alternative products, one causing exon 20 skipping and leading to a premature stop codon at codon 1737 and the other having retention of exon 20 and leading to a stop codon at codon 1767. The variant was identified in the UMD database 3 times as causal and in the BIC database 43 times as being clinically important. Easton et al (2007) report this variant as having >10e11 odds in favour of causality. Furthermore, this variant occurs within the +1 position of the 3' consensus splice site and variants at this position are a known mechanism of mutation and the type of variant expected to cause the disorder. In addition, in-silico or computational prediction software (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predicts a greater than 10% difference in splicing in 5 of 5 different programs. In summary, based on the above information, this variant is classified as 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

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.38	D
BayesDel_noAF	Pathogenic	0.30
CADD	Pathogenic	29
DANN	Uncertain	0.99
Eigen	Pathogenic	1.0
Eigen_PC	Pathogenic	0.86
FATHMM_MKL	Pathogenic	0.97	D
GERP RS		5.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.8

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.93
SpliceAI score (max)		0.99		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.99		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: rs80358150; hg19: chr17-41209068; COSMIC: COSV58785677;