rs80358042

chr17-43106455-C-Achr17-43106455-C-Gchr17-43106455-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>T 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:13 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-A is Pathogenic according to our data. Variant chr17-43106455-C-A is described in ClinVar as [Pathogenic]. Clinvar id is 54465.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr17-43106455-C-A is described in Lovd as [Pathogenic]. Variant chr17-43106455-C-A is described in Lovd as [Pathogenic]. Variant chr17-43106455-C-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.02e-7 AC: 1 AN: 1423700 Hom.: 0 Cov.: 27 AF XY: 0.00000141 AC XY: 1 AN XY: 710042

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: 9.26e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:13 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 1 Pathogenic:6 Other:1

Pathogenic, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA1)	Jun 21, 1999	- -
Pathogenic, no assertion criteria provided	clinical testing	Sharing Clinical Reports Project (SCRP)	Jun 04, 2012	- -
Pathogenic, criteria provided, single submitter	clinical testing	Counsyl	Dec 28, 2017	- -
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 = 0.998791 -
not provided, no classification provided	in vitro	Brotman Baty Institute, University of Washington	-	- -
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	All of Us Research Program, National Institutes of Health	Jan 05, 2024	The c.212+1G>T variant of the BRCA1 gene is expected to affect mRNA splicing and result in an absent or disrupted protein product. This variant has been reported in multiple individuals with breast, ovarian and/or prostate cancer (PMID: 9333265, 11802209, 22516946, 22970155, 26848529, 28724667, 29752822, 29770616, 30702160). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Truncating variants in BRCA1 are known to be pathogenic (PMID: 21989022, 17661172, 22762150). Therefore, the c.212+1G>T variant of the BRCA1 gene is classified as pathogenic. -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	GeneKor MSA	Jan 01, 2020	This variant occurs in the first base of intron 4 of the BRCA1 gene. This position is conserved in the human and other genomes and might be involved in mRNA processing. Therefore, this variant is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant is also known as IVS5+1G>T in the literature. This variant has been reported in the literature in individuals and families with breast and/or ovarian cancer (PMID: 9333265, 11802209) as well as in an individual with prostate cancer (PMID: 22516946). The mutation database ClinVar contains entries for this variant (Variation ID: 54465). -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Apr 06, 2017	This variant is denoted BRCA1 c.212+1G>T or IVS4+1G>T and consists of a G>T nucleotide substitution at the +1 position of intron 4 of the BRCA1 gene. This variant is also known as BRCA1 331+1G>T or IVS5+1G>T using alternate nomenclature. The variant destroys a canonical splice donor site and has been shown to increase the usage of an upstream cryptic splice site and result in a truncated protein (Meindl 2002, Wappenschmidt 2012). This variant has been reported in high-risk breast and/or ovarian cancer families and in at least one prostate cancer case (Shattuck-Eidens 1997, Saxena 2002, Kwong 2012, Leongamornlert 2012). We consider this variant to be pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Sep 26, 2023	The c.212+1G>T intronic pathogenic mutation results from a G to T substitution one nucleotide after coding exon 3 of the BRCA1 gene. This alteration has been identified in many, primarily Chinese, breast and/or ovarian and prostate cancer cohorts (Shattuck-Eidens et al. JAMA. 1997; 278:1243-1250; Choi MC et al. J Gynecol Oncol, 2018 Jul;29:e43; Li JY et al. Int. J. Cancer, 2019 01;144:281-289; Bhaskaran SP et al. Int. J. Cancer, 2019 Aug;145:962-973; Sun J et al. Clin. Cancer Res., 2017 Oct;23:6113-6119; Shi T et al. Int. J. Cancer, 2017 05;140:2051-2059; Leongamornlert D et al. Br. J. Cancer, 2012 May;106:1697-701). RNA experiments have shown that this alteration leads to the use of a cryptic splice donor site 22 nucleotides upstream of the native, leading to an out of frame transcript with a predicted alternate stop codon (Ambry internal data; Meindl et al. Int. J. Cancer. 2002; 97: 472–480). Close match substitutions at this position have shown the same splice defect (Ambry internal data; Houdayer C et al. Hum. Mutat., 2012 Aug;33:1228-38; Friedman LS et al. Am. J. Hum. Genet., 1995 Dec;57:1284-97; Menéndez M et al. Breast Cancer Res. Treat., 2012 Apr;132:979-92Sanz DJ et al. Clin. Cancer Res., 2010 Mar;16:1957-67). This nucleotide position is highly conserved in available vertebrate species. 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. Based on the majority of available evidence to-date, this alteration is classified as a disease-causing mutation. -
Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Oct 25, 2021	This variant causes a G to T nucleotide substitution at the +1 position of intron 4 of the BRCA1 gene. RNA studies of this variant and two different SNV that disrupt c.212+1G found aberrant splicing resulting in the deletion of 22 nucleotides from the 3' end of the exon, which is predicted to cause frameshift and nonsense-mediated decay (PMID: 11802209, 23239986). This variant has intermediate impact on BRCA1 function in a haploid human cell proliferation assay (PMID: 30209399). This variant has been reported in individuals affected with breast and ovarian cancer (PMID: 9333265, 11802209, 12442273, 22970155, 28724667, 2975282, 29770616, 33471991; Eniu et al, 2017 poster, Annals of Oncology v43-v67. 10.1093/annonc/mdx362; Gomez-Flores-Ramos et al, 2020, doi: 10.20944/preprints202008.0718.v1; Color internal data) and an individual with prostate cancer (PMID: 22516946). 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:2

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	Invitae	Apr 27, 2023	For these reasons, this variant has been classified as Pathogenic. This variant disrupts the c.212+1G nucleotide in the BRCA1 gene. Other variant(s) that disrupt this nucleotide have been determined to be pathogenic (PMID: 12955716, 19941167, 20215541, 23239986). This suggests that this nucleotide is clinically significant, and that variants that disrupt this position are likely to be disease-causing. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 54465). This variant is also known as IVS5+1G>T. Disruption of this splice site has been observed in individual(s) with clinical features of BRCA1-related conditions (PMID: 9333265, 11802209, 22516946, 22970155, 26848529). This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 4 of the BRCA1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in BRCA1 are known to be pathogenic (PMID: 20104584). -

Malignant tumor of breast Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

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The c.212+1G>T variant was identified in 2 of 3574 proband chromosomes (frequency: 0.001) from individuals or families with hereditary breast and ovarian cancer (Meindl 2002, Shattuck-Eidens 1997). The variant was also identified in dbSNP (ID: rs80358042) “With pathogenic allele”, Clinvitae database (1X as pathogenic), LOVD, ARUP Laboratories BRCA Mutations Database (as definitely pathogenic), the ClinVar database (classified as a pathogenic variant) and the BIC database (5X with clinical importance). The c.212+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	0.41	D
BayesDel_noAF	Pathogenic	0.35
Cadd	Pathogenic	32
Dann	Uncertain	0.99
Eigen	Pathogenic	1.0
Eigen_PC	Pathogenic	0.86
FATHMM_MKL	Uncertain	0.97	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;