17-43106455-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.212+1G>A variant causes a splice donor change. The variant allele was found at a frequency of 0.000000702 in 1,423,700 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: 32)
  • Exomes 𝑓: 7.0e-7 (0 hom.)
• Consequence: BRCA1 NM_007294.4 splice_donor
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic reviewed by expert panel P:17 O:1
• Conservation: PhyloP100: 4.11

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 0.013769671 fraction of the gene. Cryptic splice site detected, with MaxEntScore 4.8, offset of 12, new splice context is: ttgGTaatg. Cryptic site results in inframe change. If cryptic site found is not functional and variant results in exon loss, it results in 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 17-43106455-C-T is Pathogenic according to our data. Variant chr17-43106455-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 37446.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr17-43106455-C-T is described in Lovd as [Pathogenic]. Variant chr17-43106455-C-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRCA1	NM_007294.4	c.212+1G>A		splice_donor_variant		ENST00000357654.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRCA1	ENST00000357654.9	c.212+1G>A		splice_donor_variant		1	NM_007294.4	P4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000401 AC: 1 AN: 249638 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 134956

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000292

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: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 7.02e-7 AC: 1 AN: 1423700 Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0 AN XY: 710042

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000225

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: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:17 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 1 Pathogenic:7 Other:1

Pathogenic, reviewed by expert panel	curation	Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)	Jun 18, 2019	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 = 0.999995 -
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, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA1)	May 29, 2002	- -
not provided, no classification provided	in vitro	Brotman Baty Institute, University of Washington	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Oct 16, 2023	- -
Pathogenic, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA1)	Sep 04, 1997	- -
Pathogenic, no assertion criteria provided	clinical testing	Sharing Clinical Reports Project (SCRP)	Oct 18, 2012	- -
Pathogenic, criteria provided, single submitter	clinical testing	Counsyl	Nov 17, 2015	- -

Hereditary breast ovarian cancer syndrome Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Oct 28, 2019	Variant summary: BRCA1 c.212+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: Five predict the variant abolishes a 5 splicing donor site. A functional study, Houdayer_2012, confirmed these predictions. The variant allele was found at a frequency of 4e-06 in 249638 control chromosomes (gnomAD). c.212+1G>A has been reported in the literature in multiple individuals affected with Hereditary Breast and Ovarian Cancer (Diez_2003, Lang_2017, Kim_2012, Rebbeck_2018). These data indicate that the variant is very likely to be associated with disease. Five ClinVar submissions (evaluation after 2014) cites the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 22, 2024	This sequence change affects a donor splice site in intron 4 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 present in population databases (rs80358042, gnomAD 0.003%). Disruption of this splice site has been observed in individual(s) with breast and/or ovarian cancer (PMID: 8533757, 20215541, 23479189, 28477318). ClinVar contains an entry for this variant (Variation ID: 37446). Studies have shown that disruption of this splice site results in activation of a cryptic splice site and introduces a premature termination codon (PMID: 20215541, 22505045; Invitae). The resulting mRNA is expected to undergo nonsense-mediated decay. 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	National Health Laboratory Service, Universitas Academic Hospital and University of the Free State	Nov 16, 2021	- -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Dec 12, 2022	Canonical splice site variant demonstrated to result in aberrant splicing in a gene for which loss of function is known mechanism of disease (Sanz et al., 2010, Houdayer et al., 2012; Menendez et al., 2012); Observed in individuals with BRCA1-related cancers (Esteban Cardenosa et al., 2010; Menendez et al., 2012; Wappenschmidt et al., 2012; de Juan Jimenez et al., 2013; Gabaldo Barrios et al., 2017); Published functional studies demonstrate a damaging effect: variant classified as non-functional based on a saturation genome editing (SGE) assay measuring cell survival (Findlay et al., 2018); Not observed at significant frequency in large population cohorts (gnomAD); Also known as 331+1G>A and IVS5+1G>A; This variant is associated with the following publications: (PMID: 12955716, 25863477, 29088781, 28985766, 22505045, 23348723, 25525159, 16758124, 27836010, 28477318, 26071757, 28205045, 21735045, 27886673, 23479189, 25085752, 18279628, 20033483, 26026974, 26483394, 23233716, 22798144, 25236687, 23239986, 28918466, 31131967, 29922827, 30702160, 29446198, 30720243, 32341426, 31825140, 34413315, 28888541, 20104584, 24389207, 30209399, 8533757, 20215541) -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Jul 19, 2019	This variant is located in a canonical splice-donor site and interferes with normal BRCA1 mRNA splicing (PMID: 22505045 (2012), 20215541 (2010)). This variant has been reported in individuals affected with breast and/or ovarian cancer in the published literature (PMID: 28294317 (2017), 23479189 (2013), 22505045 (2012), 8533757 (1995)). Based on the available information, this variant is classified as pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Mar 23, 2021	This variant causes a G to A nucleotide substitution at the +1 position of intron 4 of the BRCA1 gene. RNA studies showed this variant resulted in the use of a cryptic splice donor site in exon 4 creating a premature translation termination signal and the in-frame skipping of exon 4 impacting the RING domain (PMID: 8533757, 20215541, 31843900). A functional study reported that this variant impacts BRCA1 function in a haploid human cell proliferation assay (PMID: 30209399). This variant has been detected in multiple individuals and families affected with breast and ovarian cancer (PMID: 8533757, 20215541, 22798144, 23479189, 28294317), and has been found to segregate with disease in families with a segregation likelihood ratio for pathogenicity of 1794.1757 (PMID: 8533757, 31131967). This variant has been identified in 1/249638 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	Oct 19, 2023	The c.212+1G>A intronic pathogenic mutation results from a G to A substitution one nucleotide after coding exon 3 of the BRCA1 gene. This mutation has been reported in multiple breast and/or ovarian cancer families (Friedman LS et al. Am J Hum Genet. 1995 Dec;57(6):1284-97; de Juan Jiménez I et al. Fam Cancer. 2013 Dec;12(4):767-77; Rebbeck TR et al. Hum. Mutat. 2018 05;39:593-620). Several studies have shown that this alteration leads to the deletion of the last 22 base pairs of coding exon 3 and creates a premature termination codon (Ambry internal data; Friedman LS et al. Am J Hum Genet. 1995 Dec;57(6):1284-97; Menéndez M et al. Breast Cancer Res Treat. 2012 Apr;132(3):979-92; Houdayer C et al. Hum Mutat. 2012 Aug;33(8):1228-38; Sanz DJ et al. Clin. Cancer Res., 2010 Mar;16:1957-67). 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). A multifactorial likelihood ratio analysis, which included segregation, pathology, co-occurrence, and family history data, determined that this alteration is pathogenic (Parsons MT et al. Hum. Mutat. 2019 09;40(9):1557-1578). Of note, this mutation is also designated as IVS5+1G>A in published literature. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. 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. -

Breast and/or ovarian cancer Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Foulkes Cancer Genetics LDI, Lady Davis Institute for Medical Research

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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

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.34	D
BayesDel_noAF	Pathogenic	0.34
Cadd	Pathogenic	31
Dann	Uncertain	0.99
Eigen	Pathogenic	1.0
Eigen_PC	Pathogenic	0.86
FATHMM_MKL	Uncertain	0.96	D
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D
GERP RS		4.6
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.9

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.93
SpliceAI score (max)		0.65		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.65		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: rs80358042; hg19: chr17-41258472; COSMIC: COSV100523770; COSMIC: COSV100523770;