rs879254224

Variant names:

• chr17-43099892-GGTAAAGAACA-G
• rs879254224
• NM_007294.4:c.442-22_442-13delTGTTCTTTAC

Variant summary

Our verdict is Pathogenic. The variant received 10 ACMG points: 10P and 0B. PVS1_Strong PP1_Strong PP4_Moderate

This summary comes from the ClinGen Evidence Repository: The c.442-22_442-13del variant is an intronic variant occurring in intron 6 of the BRCA1 gene. This deletion variant was not observed in gnomAD v2.1 (exomes only, non-cancer subset) or gnomAD v3.1 (non-cancer subset), but PM2_Supporting was not applied since recall is suboptimal for this type of variant (PM2_Supporting not met). This variant is reported to result in aberrant mRNA splicing. RT-PCR and qPCR assays demonstrated that the variant impacts splicing by activation of a cryptic acceptor site, resulting in a 59nt intron retention of intron 6. Combination of non-allele specific assay results (PMIDs: 10323242, 32745242) and assessment of full-length transcript quantification by real-time PCR in carriers (personal communication) suggests a near complete splicing effect. Appropriate code strength determined by comparison of results to PVS1 decision tree and assessment of mRNA splicing data (PVS1_Strong (RNA) met). Cosegregation analysis of family(ies) carrying this variant provided evidence towards pathogenicity, and has a Bayes Score of 48.83, within the thresholds for strong pathogenic evidence (LR >18.7 & ≤350) (PP1_Strong met; PMID:32745242, Internal lab contributors). Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 4.83 (based on Pathology LR=4.83), within the thresholds for Moderate evidence towards pathogenicity (LR >4.3 & ≤18.7) (PP4_Moderate met; 32745242, Internal lab contributors). In summary, this variant meets the criteria to be classified as a Pathogenic variant for BRCA1-related cancer predisposition based on the ACMG/AMP criteria applied as specified by the ENIGMA BRCA1/2 VCEP (PVS1_Strong (RNA), PP1_Strong, PP4_Moderate). LINK:https://erepo.genome.network/evrepo/ui/classification/CA10584575/MONDO:0011450/092

• Frequency: Genomes: not found (cov: 31)
• Consequence: BRCA1 NM_007294.4 intron
• Clinical Significance: Pathogenic reviewed by expert panel P:7
• Conservation: PhyloP100: 3.57
• Publications: 1 publications found

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]

BRCA1 Gene-Disease associations (from GenCC):

• breast-ovarian cancer, familial, susceptibility to, 1

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, ClinGen, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
• Fanconi anemia, complementation group S

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae), ClinGen, Ambry Genetics
• pancreatic cancer, susceptibility to, 4

  Inheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
• hereditary breast ovarian cancer syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• Fanconi anemia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Pathogenic. The variant received 10 ACMG points.

• PVS1: For more information check the summary or visit ClinGen Evidence Repository.
• PP1: For more information check the summary or visit ClinGen Evidence Repository.
• PP4: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRCA1	NM_007294.4	c.442-22_442-13delTGTTCTTTAC		intron_variant	Intron 6 of 22	ENST00000357654.9	NP_009225.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRCA1	ENST00000357654.9	c.442-22_442-13delTGTTCTTTAC		intron_variant	Intron 6 of 22	1	NM_007294.4	ENSP00000350283.3

Frequencies

GnomAD3 genomes Cov.: 31

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 31

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:7

Revision: reviewed by expert panel

Submissions by phenotype

Hereditary cancer-predisposing syndrome Pathogenic:2

Dec 20, 2024

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.442-22_442-13del10 intronic pathogenic mutation, located in intron 5 of the BRCA1 gene, results from a deletion of 10 nucleotides within intron 5 of the BRCA1 gene. This alteration is identified in numerous individuals with a clinical history of breast and/or ovarian cancer and it segregates with disease in multiple families (Lin PH et al. Oncotarget, 2016 Feb;7:8310-20; Wong ES et al. PLoS One, 2015 Jul;10:e0134408; Ang P et al. Cancer Epidemiol Biomarkers Prev, 2007 Nov;16:2276-84; Li SS et al. Hum Genet, 1999 Mar;104:201-4). This nucleotide position is not well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration may result in the creation or strengthening of a novel splice acceptor site. This alteration leads to the use of a cryptic acceptor site within intron 5 leading to a partial inclusion of this intron and a protein with a premature termination codon (Ambry internal data; Li SS et al. Hum Genet, 1999 Mar;104:201-4; Ang P et al. Cancer Epidemiol Biomarkers Prev, 2007 Nov;16:2276-84). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Sep 11, 2023

Color Diagnostics, LLC DBA Color Health

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant causes a 10 nucleotide deletion near the splice acceptor site in intron 6 of the BRCA1 gene. Splice site prediction tools predict that this variant may have a significant impact on RNA splicing. RNA studies on carrier-derived RNA has shown an out-of-frame splicing associated with variant (PMID: 10323242, 18006916, 32745242). Moreover, cellular characterization on ex vivo cells derived from carriers showed sensitivity to PARP inhibitor and other cellular features consistent with compromised BRCA1 function in the normal cellular response to DNA damage and DNA replication blockage (32745242). This variant has been reported in over 10 individuals affected with breast and/or ovarian cancer (PMID: 10323242, 18006916, 26824983, 32745242, 34503154), and a haplotype analysis suggests that this variant may be founder mutation among Han Chinese (PMID: 32745242). This variant also has been reported to segregate with breast and ovarian cancers in at least five carrier families (PMID: 10323242, 32745242). 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

Oct 31, 2018

Cancer Variant Interpretation Group UK, Institute of Cancer Research, London

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Data used in classification: The variant was observed in 2 independent UK families undergoing clinical diagnostic testing. Denominator ~16,600. In the GNOMAD NFE population of 63,369 individuals, the frequency of this variant is 0. exact: p=0.04. (PS4_strong) This variant is reported twice on ClinVar. There are additional reports of this variant in: i) Li et al. 1999 Hum Genet 104 201-204: Variant found variant in 2 unrelated Taiwanese families:Br Ca in mother and daughter (age 58 & 28), Br Ca/Ov Ca in mother age 48 and Br Ca in daughter (age 30). ii) Ang et al Cancer Epidem Bio and Prev 2007; 16 (11) two affected sisters. In the remainder of the GNOMAD populations (75,263 individuals, including 8624 East Asians), the frequency of this variant is 0 (PM2). Li et al. 1999 Hum Genet 104 201-204: RT-PCR carried out: an insertion of 59 nucleotides mRNA results in frameshift and premature termination codon in exon 8 (historical exon numbering). AND Ang et al Cancer Epidem Bio and Prev 2007; 16 (11): insertion of 59 nucleotides mRNA. However, only single WT control used. (PS3_mod) Data not included in classification: Li et al. 1999 Hum Genet 104 201-204: variant segregates with disease in two 2 case families. In silico analysis predict effect on splicing: Predicted change at acceptor site 13 bps downstream. MaxEnt: -43.6%; NNSPLICE: -65.0% Other information: Wong et al. 2015 (PLOS1). Patient had a BRCA1 c.442-22-442-13 variant and also a pathogenic variant in BRCA2 c.5645C>A; p.Ser1882*). -

Dec 09, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change falls in intron 6 of the BRCA1 gene. It does not directly change the encoded amino acid sequence of the BRCA1 protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or altered protein product. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with breast and/or ovarian cancer (PMID: 10323242, 18006916, 26221963, 26824983; internal data). It is commonly reported in individuals of Asian ancestry (PMID: 10323242, 18006916, 26221963, 26824983; internal data). This variant is also known as IVS7-15del10, IVS7-22del10, and g.41251910_41251919 delGTAAAGAACA. ClinVar contains an entry for this variant (Variation ID: 246362). Studies have shown that this variant results in insertion of 59 bp in intron 7, and produces a non-functional protein and/or introduces a premature termination codon (PMID: 10323242, 18006916). For these reasons, this variant has been classified as Pathogenic. -

BRCA1-related cancer predisposition Pathogenic:1

Jun 11, 2024

ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen

Significance: Pathogenic

Review Status: reviewed by expert panel

Collection Method: curation

The c.442-22_442-13del variant is an intronic variant occurring in intron 6 of the BRCA1 gene. This deletion variant was not observed in gnomAD v2.1 (exomes only, non-cancer subset) or gnomAD v3.1 (non-cancer subset), but PM2_Supporting was not applied since recall is suboptimal for this type of variant (PM2_Supporting not met). This variant is reported to result in aberrant mRNA splicing. RT-PCR and qPCR assays demonstrated that the variant impacts splicing by activation of a cryptic acceptor site, resulting in a 59nt intron retention of intron 6. Combination of non-allele specific assay results (PMIDs: 10323242, 32745242) and assessment of full-length transcript quantification by real-time PCR in carriers (personal communication) suggests a near complete splicing effect. Appropriate code strength determined by comparison of results to PVS1 decision tree and assessment of mRNA splicing data (PVS1_Strong (RNA) met). Cosegregation analysis of family(ies) carrying this variant provided evidence towards pathogenicity, and has a Bayes Score of 48.83, within the thresholds for strong pathogenic evidence (LR >18.7 & <=350) (PP1_Strong met; PMID: 32745242, Internal lab contributors). Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 4.83 (based on Pathology LR=4.83), within the thresholds for Moderate evidence towards pathogenicity (LR >4.3 & <=18.7) (PP4_Moderate met; 32745242, Internal lab contributors). In summary, this variant meets the criteria to be classified as a Pathogenic variant for BRCA1-related cancer predisposition based on the ACMG/AMP criteria applied as specified by the ENIGMA BRCA1/2 VCEP (PVS1_Strong (RNA), PP1_Strong, PP4_Moderate). -

Familial cancer of breast;C2676676:Breast-ovarian cancer, familial, susceptibility to, 1;C4554406:Fanconi anemia, complementation group S Pathogenic:1

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Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Pathogenic:1

Dec 12, 2019

GeneDx

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Non-canonical splice site variant demonstrated to result in the insertion of 59 nucleotides, leading to protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease (Li 1999, Ang 2007); Observed in individuals with a personal or family history consistent with pathogenic variants in this gene (Li 1999, Ang 2007, Lin 2016); Not observed in large population cohorts (Lek 2016); Also known as 561-22_561-13del10 or IVS7-22_IVS7-13del10; This variant is associated with the following publications: (PMID: 26824983, 10323242, 18006916) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.6
Mutation Taster		=3/97	disease causing (ClinVar)

Splicing

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

Other links and lift over

dbSNP: rs879254224; hg19: chr17-41251909;