chr17-43057050-AC-A

Position:

• chr17-43057050-AC-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+1delG variant causes a splice donor, intron change. The variant was absent in control chromosomes in GnomAD project. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: BRCA1 NM_007294.4 splice_donor, intron
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:11
• 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 0.014842632 fraction of the gene. No cryptic splice site detected. Exon removal is inframe change.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 17-43057050-AC-A is Pathogenic according to our data. Variant chr17-43057050-AC-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 91644.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-43057050-AC-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRCA1	NM_007294.4	c.5277+1delG		splice_donor_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.5277+1delG		splice_donor_variant, intron_variant		1	NM_007294.4	ENSP00000350283.3

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 31

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:11

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

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

Pathogenic, criteria provided, single submitter	research	HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology	Jul 22, 2019	- -
Pathogenic, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA1)	Dec 23, 2003	- -
Pathogenic, no assertion criteria provided	clinical testing	Sharing Clinical Reports Project (SCRP)	Nov 16, 2010	- -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Feb 21, 2024	- -
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 Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	May 05, 2021	This variant disrupts a canonical splice-donor site and interferes with normal BRCA1 mRNA splicing. This variant has not been reported in large, multi-ethnic general populations (Genome Aggregation Database, http://gnomad.broadinstitute.org). In the published literature, this variant has been reported in a family affected with hereditary breast/ovarian cancer as well as individuals who underwent genetic testing (PMID: 16267036 (2005), 29446198 (2018)). Based on the available information, this variant is classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Sep 28, 2023	Canonical splice site variant predicted to result in an in-frame loss of the adjacent exon in a gene for which loss of function is a known mechanism of disease; Observed in an individual with triple negative breast cancer (Villarreal-Garza et al., 2021); Deletions involving coding exons of this gene are a known mechanism of disease (HGMD); Not observed at significant frequency in large population cohorts (gnomAD); Disrupts the critical BRCT 2 domain (UniProt); Also known as 5396+1delG; IVS20+1delG; This variant is associated with the following publications: (PMID: 28152038, 22535016, 30787465, 35875314, 25348405, 29446198, 16267036, 33287145) -

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Jun 14, 2023	The c.5277+1delG intronic pathogenic mutation, located in intron 18 of the BRCA1 gene, results from a deletion of one nucleotide within intron 18 of the BRCA1 gene. This nucleotide position is highly conserved in available vertebrate species. This mutation has been identified in a Hispanic family with HBOC (Rebbeck TR et al. Hum Mutat, 2018 05;39:593-620). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). In silico splice site analysis predicts that this alteration will weaken the native splice donor site and will result in the creation or strengthening of a novel splice donor site. 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, however, direct evidence is insufficient at this time (Ambry internal data). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Feb 01, 2023	This variant causes a deletion of 1-nucleotide in the intron 19 splice donor site of the BRCA1 gene. Splice site prediction tools predict that this variant has a significant impact on RNA splicing by disrupting the splice donor site and the creation of a cryptic donor site that would result in out-of-frame splicing. Although RNA studies have not been reported for this variant, this variant is expected to result in an absent or non-functional protein product. Canonical splice site variants at this donor site, c.5277+1G>A and c.5277+1G>T, have been reported as disease-causing in ClinVar due to evidence of RNA splicing defect, reports in multiple individuals and families affected with breast and ovarian cancer and loss-of-function in experimental functional study (ClinVar variation ID: 37654, 462668). This variant has been reported in an individual affected with triple-negative breast cancer (PMID: 35875314) and in suspected hereditary breast and ovarian cancer families (PMID: 29446198; ClinVar RCV000077161.9, RCV000236858.5). This variant also has been reported in an individual with a BRCA2 deleterious truncation covariant who was affected with ovarian and colorectal cancer (PMID: 22535016). 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 Likely Pathogenic. -

Hereditary breast ovarian cancer syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Oct 05, 2023	This sequence change affects a splice site in intron 19 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 not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with breast and/or ovarian cancer (PMID: 11149413, 11802208, 11802209, 29446198, 30720863). ClinVar contains an entry for this variant (Variation ID: 91644). Studies have shown that disruption of this splice site results in skipping of exon 20 (also known as exon 19), but is expected to preserve the integrity of the reading-frame (PMID: 24667779). This variant disrupts the p.Gly1738 amino acid residue in BRCA1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 15353005, 16489001, 17453335, 17902052, 18465347, 21918854, 23113073, 23536787, 24010542). 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, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Nov 14, 2022	Variant summary: BRCA1 c.5277+1delG 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: Three predict the variant weakens the canonical 5' splicing donor site. Two predict the variant abolishes the canonical 5' splicing donor site. However, these predictions have yet to be confirmed by functional studies. The variant was absent in 251494 control chromosomes. c.5277+1delG has been reported in the literature in individuals affected with features of Hereditary Breast And Ovarian Cancer, in a reference laboratory testing cohort and in at-least one report of its occurrence in settings of Triple Negative Breast Cancer (TNBC) (example, Judkins_2005, Heidemann_2012, LaDuca_2014, Rebbeck_2018, Vietri_2020, Villarreal-Garza_2021). One of these citations reported this variant in double heterozygosity with another pathogenic variant in the BRCA2 gene in one family (BRCA2, c.658_659delGT;p.Val220IlefsX4, Heidemann_2012 cited in Vietri_2020). The double heterozygous carrier in this family developed coecum cancer by age 58 and ovarian cancer by age 61. A sister and niece are carriers of this variant but not the BRCA2 variant and were reportedly unaffected by the ages of 58 and 28 years respectively. These data indicate that the variant is likely to be associated with disease with a variable penetrance. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Six clinical diagnostic laboratories and one consortium (CIMBA) 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

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		1.0		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.84		Position offset: 3
DS_DL_spliceai		1.0		Position offset: 2

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

Publications

LitVar

Other links and lift over

dbSNP: rs273901754; hg19: chr17-41209067;