rs397509266

chr17-43049200-A-Cchr17-43049200-A-Gchr17-43049200-A-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2 PP5 BP4

The NM_007294.4(BRCA1):c.5333-6T>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency: Genomes: not found (cov: 31)
• Consequence: BRCA1 NM_007294.4 splice_region, splice_polypyrimidine_tract, intron
• Scores: Splicing: ADA: 0.9289
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:5 U:2 O:2
• Conservation: PhyloP100: -2.00

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 17-43049200-A-C is Pathogenic according to our data. Variant chr17-43049200-A-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 55538.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=4, Uncertain_significance=2, not_provided=2, Pathogenic=1}.
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).. Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRCA1	NM_007294.4	c.5333-6T>G		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000357654.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRCA1	ENST00000357654.9	c.5333-6T>G		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_007294.4	P4

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 31

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:5 Uncertain:2 Other:2

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 1 Pathogenic:2 Other:1

Likely pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Dec 01, 2022	- -
not provided, no classification provided	in vitro	Brotman Baty Institute, University of Washington	-	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Jan 08, 2024	This variant causes a T to G nucleotide substitution at the -6 position of intron 20 of the BRCA1 gene. Splice site prediction tools predict that this variant may have a significant impact on RNA splicing. An RNA study has reported that this variant causes the out-of-frame skipping of exon 21 (PMID: 11802209) and this variant also has been reported in ClinVar to cause abnormal splicing (SCV002646843.1). A functional assay that required proper splicing for the measured activity has reported that this variant impacts BRCA1 function in a haploid cell proliferation assay (PMID: 30209399). Since this variant does not directly impact the coding sequence, the splicing prediction, RNA data and functional data could be interpreted together as evidence for a significant disruption in RNA processing. This variant has been detected in an individual affected with breast cancer and reported in two families affected with breast cancer and both breast and ovarian cancer (PMID: 11802209; Color internal data). A multifactorial analysis has reported likelihood ratios for pathogenicity based on segregation and tumor pathology of 0.6846 and 3.73, respectively (PMID: 31131967). 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 cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Jan 18, 2021	The c.5333-6T>G intronic pathogenic mutation results from a T to G substitution 6 nucleotides upstream from coding exon 20 in the BRCA1 gene. This nucleotide position is well conserved in available vertebrate species. This alteration was detected in 1/989 unrelated individuals from a cohort of German breast and/or ovarian cancer families (Meindl A et al. Int. J. Cancer. 2002 Feb;97:472-80). RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data; Meindl A et al. Int. J. Cancer. 2002 Feb;97:472-80). One study found that this nucleotide substitution is non-functional in a high throughput genome editing haploid cell survival assay (Findlay GM et al. Nature. 2018 10;562:217-222). In addition, was called likely pathogenic based on multifactorial likelihood analysis (Parsons MT et al. Hum. Mutat. 2019 09;40:1557-1578). In silico splice site analysis predicts that this alteration may weaken the native splice acceptor site and will result in the creation or strengthening of a novel splice acceptor site. 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	Nov 16, 2023	This variant causes a T to G nucleotide substitution at the -6 position of intron 20 of the BRCA1 gene. Splice site prediction tools predict that this variant may have a significant impact on RNA splicing. An RNA study has reported that this variant causes the out-of-frame skipping of exon 21 (PMID: 11802209) and this variant also has been reported in ClinVar to cause abnormal splicing (SCV002646843.1). A functional assay that required proper splicing for the measured activity has reported that this variant impacts BRCA1 function in a haploid cell proliferation assay (PMID: 30209399). Since this variant does not directly impact the coding sequence, the splicing prediction, RNA data and functional data could be interpreted together as evidence for a significant disruption in RNA processing. This variant has been detected in an individual affected with breast cancer and reported in two families affected with breast cancer and both breast and ovarian cancer (PMID: 11802209; Color internal data). A multifactorial analysis has reported likelihood ratios for pathogenicity based on segregation and tumor pathology of 0.6846 and 3.73, respectively (PMID: 31131967). 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. -

not provided Pathogenic:1 Uncertain:1

Uncertain significance, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Nov 17, 2020	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jun 01, 2021	- -

Hereditary breast ovarian cancer syndrome Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Invitae

May 01, 2021

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. Experimental studies have shown that this variant affects BRCA1 protein function (PMID: 30209399). This variant has been observed in individual(s) with a personal and/or family history of breast and ovarian cancer (PMID: 11802209). This variant is also referred to as IVS21-6T>G in the literature. ClinVar contains an entry for this variant (Variation ID: 55538). This variant is not present in population databases (ExAC no frequency). This sequence change falls in intron 20 of the BRCA1 gene. It does not directly change the encoded amino acid sequence of the BRCA1 protein. -

Familial cancer of breast Other:1

not provided, no classification provided

literature only

ClinVar Staff, National Center for Biotechnology Information (NCBI)

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	11
Dann	Benign	0.54
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.93
dbscSNV1_RF	Benign	0.38
SpliceAI score (max)		0.79		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.79		Position offset: -1
DS_AL_spliceai		0.41		Position offset: -6

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

Publications

LitVar

Other links and lift over

dbSNP: rs397509266; hg19: chr17-41201217;