17-43057051-C-T

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PVS1_Moderate PM2 PP3_Strong PP5_Very_Strong

The NM_007294.4(BRCA1):c.5277+1G>A variant causes a splice donor 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
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic reviewed by expert panel P:27 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 16 ACMG points.

• PVS1: Splicing variant, NOT destroyed by nmd, known LOF gene, truncates exone, which is 0.014842632 fraction of the gene. No cryptic splice site detected. Exon removal is inframe change.
• 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 17-43057051-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/exons	MANE	UniProt
BRCA1	NM_007294.4	c.5277+1G>A		splice_donor_variant		ENST00000357654.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRCA1	ENST00000357654.9	c.5277+1G>A		splice_donor_variant		1	NM_007294.4	P4

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:27 Other:2

Revision: reviewed by expert panel

Submissions by phenotype

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

Pathogenic, criteria provided, single submitter	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	Oct 08, 2014	- -
Pathogenic, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA1)	Dec 30, 1999	- -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Jul 20, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Jul 19, 2023	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. -
not provided, no classification provided	in vitro	Brotman Baty Institute, University of Washington	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Sharing Clinical Reports Project (SCRP)	May 02, 2012	- -
Pathogenic, criteria provided, single submitter	literature only	Counsyl	Aug 19, 2014	- -
Pathogenic, criteria provided, single submitter	clinical testing	Neuberg Centre For Genomic Medicine, NCGM	-	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. -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	Sep 21, 2015	- -
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, reviewed by expert panel	curation	Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)	Aug 10, 2015	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 -
Pathogenic, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -

not provided Pathogenic:5 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Feb 20, 2019	- -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Jul 01, 2015	- -
Pathogenic, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Oct 25, 2021	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) -
Pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute	-	- -
not provided, no classification provided	in vitro	MutSpliceDB: a database of splice sites variants effects on splicing, NIH	-	- -

Hereditary breast ovarian cancer syndrome Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Feb 25, 2021	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. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Dec 30, 2023	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 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 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 introduces a premature termination codon (PMID: 24667779; Invitae). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	research	Genetics Program, Instituto Nacional de Cancer	Nov 01, 2021	- -
Pathogenic, no assertion criteria provided	research	Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto	Jan 31, 2014	- -

Hereditary cancer-predisposing syndrome Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	May 10, 2023	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. -
Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Aug 05, 2022	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. -
Pathogenic, no assertion criteria provided	clinical testing	True Health Diagnostics	Oct 30, 2017	- -

not specified Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

May 24, 2017

- -

Breast and/or ovarian cancer Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Foulkes Cancer Genetics LDI, Lady Davis Institute for Medical Research

Jan 22, 2016

- -

Malignant tumor of breast Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

-

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

Pathogenic, no assertion criteria provided

research

King Laboratory, University of Washington

Sep 01, 2019

- -

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
MutationTaster	Benign	1.0	A;A;A;A;A;A;A;A;A;A;A;A;A;A
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;