17-43095891-G-GTGGTTCCTGATTTCATCCCT

Variant names:

• chr17-43095891-G-GTGGTTCCTGATTTCATCCCT
• rs397509302
• NM_007294.4:c.624_625insAGGGATGAAATCAGGAACCA

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1 PM2

The NM_007294.4(BRCA1):​c.624_625insAGGGATGAAATCAGGAACCA​(p.Pro209ArgfsTer32) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 31)
• Consequence: BRCA1 NM_007294.4 frameshift
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.172

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 10 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRCA1	NM_007294.4	c.624_625insAGGGATGAAATCAGGAACCA	p.Pro209ArgfsTer32	frameshift_variant	Exon 9 of 23	ENST00000357654.9	NP_009225.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRCA1	ENST00000357654.9	c.624_625insAGGGATGAAATCAGGAACCA	p.Pro209ArgfsTer32	frameshift_variant	Exon 9 of 23	1	NM_007294.4	ENSP00000350283.3

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 31

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Hereditary cancer-predisposing syndrome Uncertain:1

Sep 01, 2023

Color Diagnostics, LLC DBA Color Health

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant inserts 20 nucleotides in exon 9 of the BRCA1 gene, creating a premature translation stop signal. The impacted exon is also known as exon 8 by a numbering scheme that only counts coding exon and exon 10 by Breast Cancer Information Core (BIC) nomenclature. This variant is expected to result in the absence of functional full-length protein product. A functional study has shown that this variant results in a reduced cell viability when exposed to a DNA damaging agent (Pongsavee 2017). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). This specific variant has been previously reported in an individual affected with breast and ovarian cancer (PMID: 12203997) and in an individual affect with breast cancer (PMID: 33649982). Two other truncation variants in the vicinity of exons 8 and 9 have been reported in individuals affected with high-risk breast cancer and/or ovarian cancer (PMID: 12815604, 15642173) and in a suspected hereditary breast and ovarian cancer family (PMID: 8764110). In one study, an exon 9 frameshift variant (c.594_597del) has been observed in compound heterozygosity with a known pathogenic missense variant, in an individual diagnosed with Fanconi anemia (PMID: 25472942). This truncation variant was inherited from the mother, who was personally affected with ovarian cancer at age 50 with a positive family history of disease. This presentation suggests that the exon 9 variant contributed to the development of disease. However, two splicing variants c.591C>T and c.594-2A>C that have been demonstrated to cause a premature translation stop signal and have been reported in individuals affected with breast and ovarian cancer, as well as in healthy unaffected individuals (PMID: 16211554, 19892845, 25639900, 27008870). The case-control, health history, tumor pathology and segregation data for the c.594-2A>C variant either indicate that this variant is not pathogenic or that pathogenicity is inconclusive (PMID: 25639900, 27008870). In these carriers, there is a relative increase in the skipping of exons 8 and 9 by pre-mRNA splicing that is expected to cause a small in-frame deletion of 41 amino acids from the reference protein (1884 amino acids) (PMID: 19892845, 27008870). An interpretation of these findings is that a BRCA1 mRNA isoform lacking exons 8 and 9 is normally produced and is functional. This alternate mRNA isoform is expected to be refractory to frameshift, nonsense and splicing defective variants found in exons 8 and 9 (PMID: 27008870). RNA studies have confirmed the appearance of the skipping of exons 8 and 9 in the majority of individuals tested, however, the degree of expression also appears to be highly variable in individuals (PMID: 24569164, 27008870, 28905878, 32133419). Taken together, the available evidence suggests that the expected deleterious effects of this c.624_625ins20 variant and other truncation variants occurring in exons 8 and 9 could be ameliorated by the expression of the mRNA isoform lacking exons 8 and 9 that retains normal BRCA1 function. Because of the uncertain clinical consequences of this variant, it is classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs397509302; hg19: chr17-41247908;