rs80358015

chr17-43091432-T-Cchr17-43091432-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PP3_Moderate

The NM_007294.4(BRCA1):c.4096+3A>G variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,602 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: BRCA1 NM_007294.4 splice_donor_region, intron
• Scores: Splicing: ADA: 0.9998
• Clinical Significance: Uncertain significance reviewed by expert panel P:4 U:14 B:1
• Conservation: PhyloP100: 3.20

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 4 ACMG points.

• 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRCA1	NM_007294.4	c.4096+3A>G		splice_donor_region_variant, intron_variant		ENST00000357654.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRCA1	ENST00000357654.9	c.4096+3A>G		splice_donor_region_variant, intron_variant		1	NM_007294.4	P4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000205 AC: 3 AN: 1461602 Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1 AN XY: 727064

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: 0.00000270

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Pathogenic:4 Uncertain:14 Benign:1

Revision: reviewed by expert panel

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 1 Pathogenic:3 Uncertain:6

Uncertain significance, no assertion criteria provided	clinical testing	Breast Cancer Information Core (BIC) (BRCA1)	Feb 20, 2004	- -
Uncertain significance, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Dec 13, 2023	This variant causes an A to G nucleotide substitution at the +3 position of intron 10 of the BRCA1 gene. Splice site prediction tools predict that this variant may have a significant impact on RNA splicing. An RNA study has shown splicing impacts leading to reduced wild-type transcript and two alternative transcript predicted to cause in-frame deletion, including the naturally occurring skipping of exon 10 (PMID: 23239986). This variant has been reported in individuals affected with breast and ovarian cancer (PMID: 23239986, 24728189, 28588830, 31683985) and colorectal cancer (PMID 28195393). This variant has been detected in six suspected hereditary breast and ovarian cancer pedigrees from a Danish and an Icelandic study, in which co-segregation of the variant and breast and ovarian cancer varied by pedigree and co-segregation or the lack thereof could not be definitively determined (PMID: 28588830, 31683985). Two homozygous carriers were identified, in which one was reported healthy in her fifth decade of life (PMID: 28588830) and the other was affected with lung cancer and multiple cafe-au-lait spots and was unaffected with breast or ovarian cancer (PMID: 31683985). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -
Uncertain significance, reviewed by expert panel	curation	Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)	Apr 12, 2018	Identified in a healthy homozygous carrier at age 58 with a single café au lait spot and a normal chromosomal breakage test (Byrjalsen et al., 2018 - PMID: 28588830). Clinical data collected by the ENIGMA consortium demonstrates that the BRCA1 c.4096+3A>G variant may not exhibit the clinical characteristics of a standard high-risk pathogenic BRCA1 variant (Spurdle, unpublished data). This splice site variant has been proven to result in production of naturally occurring in-frame transcripts delta11q and delta11 (Wappenschmidt et al,. 2012 - PMID: 23239986). Since no clinically relevant domain has been described in BRCA1 exon 11 (ENIGMA rules), the splicing alteration is compatible with the clinical data, and supports Class-3 classification. -
Uncertain significance, criteria provided, single submitter	clinical testing	Department of Medical Genetics, Oslo University Hospital	Aug 02, 2017	- -
Uncertain significance, no assertion criteria provided	clinical testing	BRCAlab, Lund University	Mar 02, 2020	- -
Likely pathogenic, no assertion criteria provided	clinical testing	Sharing Clinical Reports Project (SCRP)	Apr 20, 2012	- -
Pathogenic, no assertion criteria provided	research	deCODE genetics, Amgen	Jul 21, 2023	The variant NM_007294.4:c.4096+3A>G (chr17:43091432) in BRCA1 was detected in 118 heterozygotes out of 58K WGS Icelanders (MAF= 0,102%). Following imputation in a set of 166K Icelanders (313 imputed heterozygotes) we observed an association with ovarian cancer using 907 cases and 299709 controls (OR= 8.49, P= 2.97e-08) and breast cancer using 6908 cases and 292623 controls (OR= 3.13, P= 7.59e-06). Therefore, the PS4 criterion was applied. Based on RNA sequence data from 42 heterozygotes and 17,551 non-carriers, the variant associates with skipping of exon 10, consistent with its predicted functional effect (Effect (SD)= -1.45, P=2.1e-15). Therefore, the PS5 criterion was applied. This variant has been reported in ClinVar previously as a variant of uncertain significance. Based on ACMG criteria (PS4, PS5) this variant classifies as pathogenic. -
Likely pathogenic, no assertion criteria provided	clinical testing	Pathway Genomics	Jul 24, 2014	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Baylor Genetics	Mar 28, 2023	- -

not specified Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Aug 09, 2019	Variant summary: BRCA1 c.4096+3A>G alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Three predict that the variant abolishes a 5' splicing donor site. A functional study confirms that this variant compromises the existing intron 11 donor splice site resulting in a transcript lacking 3309 nucleotides from exon 11, but retaining 117 nucleotides from the 5' end of exon 11, together with increased abundance of the naturally occurring isoforms BRCA1-DELTAex11 (legacy name) (Wappenschmidt_2012). The presence of naturally occurring BRCA1 isoforms lacking exon 11 has recently been described, adding to the complexity of assessing the effect of the variant. The variant was absent in 254008 control chromosomes (gnomAD and Song_2014). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.4096+3A>G has been reported in the literature in individuals affected with Hereditary Breast and Ovarian Cancer (Judkins_2005, Borg_2010, Wappenschmidt_2012, Song_2014, Petersen_2016) and colorectal cancer (Hansen_2017), without strong evidence for pathogenicity in some studies. One study showed lack of segregation with disease for this variant in two individuals from a family with multiple cases of breast and ovarian cancer, including a healthy 58 y/o woman who was homozygous for the variant and a 47 y/o woman with breast cancer who tested negative for this variant (Byrjalsen_2017). In addition, co-occurrences with other pathogenic variants in individuals with a personal history of breast cancer have been reported (BRCA2 c.7007G>A, p.Arg2336His; ATM c.6404_6405insTT, p.Arg2136fsX1), providing supporting evidence for a benign role (Beissel_ 2014, internal testing). Eight clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar (after 2014) with conflicting interpretations (uncertain significance X6; pathogenic/ likely pathogenic X2). Based on the evidence outlined above, the variant was classified as uncertain significance until additional functional or segregation data becomes available. -
Uncertain significance, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Feb 06, 2024	- -

not provided Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Feb 21, 2023	Not observed at significant frequency in large population cohorts (gnomAD); Published functional studies demonstrate that this variant results in transcripts displaying a deletion of 3309 nucleotides from the 3' end of exon 10 and an increase in the naturally-occurring BRCA1 deletion exon 10 isoform, also reported as exon 11 using alternate nomenclature, with what appears to be some residual normal transcript production (Wappenschmidt et al., 2012); Observed in individuals with breast and/or ovarian cancer and incompletely segregates with disease in several families (Borg et al., 2010; Beissel et a., 2014; Song et al., 2014; Arason et al., 2019); In silico analysis supports a deleterious effect on splicing; Also known as BRCA1 4215+3A>G, IVS11+3A>G, and 4216nt-2A>G; This variant is associated with the following publications: (PMID: 28195393, 11431698, 28588830, 8972225, 16943438, 11359908, 20104584, 17591843, 24728189, 19383375, 26075997, 23239986, 31683985) -
Uncertain significance, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The BRCA1 c.4096+3A>G variant was identified in 3 of 8746 proband chromosomes (frequency: 0.0003) from individuals or families with breast cancer (Borg 2010, Wappenschmidt 2012, Song 2014). The variant was identified in dbSNP (rs80358015) as “with likely pathogenic allele”, ClinVar (classified as uncertain significance by Invitae, GeneDx, Ambry Genetics, Integrated Genetics and 4 other submitters, pathogenic by Lady Davis and 1 other submitter, likely pathogenic by Pathway Genomics and SCRP and likely benign by Institute of Cancer Research ), LOVD 3.0 (observed 4x) and UMD-LSDB (observed 1x). The variant was not identified in the following control databases: the Exome Aggregation Consortium (August 8th 2016), or the Genome Aggregation Database (March 6, 2019, v2.1.1). The variant was identified in our laboratory in a breast cancer family in 1 affected and 3 unaffected individuals. In addition, the variant was identified in a consanguineous family in an unaffected homozygous carrier, suggesting it may not have a clinical effect (Byrjalsen 2017). The variant causes a partial deletion of exon 10, but doesn’t fully abolish transcript production (Wappenschmidt 2012, Kim 2006, Huber 2001, Thakur 1997). The c.4096+3A>G variant is located in the 5' splice region but does not affect the invariant +1 and +2 positions. However, positions +3 to +6 are part of the splicing consensus sequence and variants involving these positions sometimes affect splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. -

Hereditary cancer-predisposing syndrome Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Mar 16, 2023	This variant causes an A to G nucleotide substitution at the +3 position of intron 10 of the BRCA1 gene. Splice site prediction tools predict that this variant may have a significant impact on RNA splicing. An RNA study has shown splicing impacts leading to reduced wild-type transcript and two alternative transcript predicted to cause in-frame deletion, including the naturally occurring skipping of exon 10 (PMID: 23239986). This variant has been reported in individuals affected with breast and ovarian cancer (PMID: 23239986, 24728189, 28588830, 31683985) and colorectal cancer (PMID 28195393). This variant has been detected in six suspected hereditary breast and ovarian cancer pedigrees from a Danish and an Icelandic study, in which co-segregation of the variant and breast and ovarian cancer varied by pedigree and co-segregation or the lack thereof could not be definitively determined (PMID: 28588830, 31683985). Two homozygous carriers were identified, in which one was reported healthy in her fifth decade of life (PMID: 28588830) and the other was affected with lung cancer and multiple cafe-au-lait spots and was unaffected with breast or ovarian cancer (PMID: 31683985). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	Ambry Genetics	Dec 11, 2023	The c.4096+3A>G intronic variant results from an A to G substitution 3 nucleotides after coding exon 9 in the BRCA1 gene. Studies from carrier blood lymphocytes have demonstrated that this alteration results in aberrant splicing leading to an increase in the amount of transcript lacking all of exon 9 (also known as Δ11) and another lacking most of the 3' end of exon 9 (also known as Δ11q and Δ11b) (Wappenschmidt B et al. PLoS ONE. 2012;7:e50800; Ambry internal data). Both of these alterations are in-frame losses and both have been reported as naturally occurring isoforms in blood and other tissues, including mammary gland (Colombo M et al. Hum. Mol. Genet. 2014 Jul;23:3666-80; Thakur S et al. Mol. Cell. Biol. 1997 Jan;17:444-52; Magdinier F et al. Oncogene. 1999 Jul;18:4039-43; Wilson CA et al. Oncogene. 1997 Jan;14:1-16). Functional studies have shown that the protein generated by the isoform lacking exon 9 is unable to form Rad51 foci and that the protein generated by both isoforms may also be mislocalized to the cytoplasm; however, not all studies agree on the latter point (Huber LJ et al. Mol. Cell. Biol. 2001 Jun;21:4005-15; Thakur S et al. Mol. Cell. Biol. 1997 Jan;17:444-52; Wilson CA et al. Oncogene. 1997 Jan;14:1-16). A homozygous knock-in mouse model of the isoform lacking exon 9 did not result in overt developmental defects; however, there were mammary gland abnormalities and spontaneous tumor formation (Kim SS et al. Mol. Cell. Biol. 2006 Sep;26:6983-92). This alteration has been reported in multiple cohorts of breast and ovarian cancer (Beissel JM et al. Gynecol Oncol Rep. 2014 Dec;10:25-7; Song H et al. Hum. Mol. Genet. 2014 Sep;23:4703-9; Borg A et al. Hum. Mutat. 2010 Mar;31:E1200-40; Machackova E et al. Klin Onkol. 2019;32:51-71; Arason A et al. Genes (Basel). 2019 11;10:); however, it was also identified in a homozygous state in an individual who was ascertained for but did not have Fanconi anemia (Byrjalsen A et al. Clin Case Rep. 2017 Jun;5:876-879). Of note, this alteration is also referred to as IVS11+3A>G in published literature. This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. Since supporting evidence is conflicting at this time, the clinical significance of this alteration remains unclear. -

Hereditary breast ovarian cancer syndrome Uncertain:1 Benign:1

Likely benign, criteria provided, single submitter	clinical testing	Cancer Variant Interpretation Group UK, Institute of Cancer Research, London	Oct 31, 2018	Data included in classification. Segregation data supporting non-pathogencity, Byrjalsen et al, Clinical case Reports, 2017. Healthy 58y Danish homozygote carrier reported by Byrjalsen et al, Clinical case Reports, 2017 (confirmed on two different genotyping methods). % change MaxEnt Score: -100, % change NNS Score: -98.22845. Alternative splicing reported in Wappenschmidt, B. et al., 2012 PLoS One 7(12). However, variants at c.4096+1 (IVS11+1), c.4096+2 (IVS11+2) are of uncertain pathogenicity on account of rescue by production of naturally occurring in-frame transcripts delta 11q (Bonatti et al., 2006) and also delta 11 (Radice, unpublished data). See ENIGMA classification rules (https://enigmaconsortium.org/wp-content/uploads/2017/12/ENIGMA_Rules_2017-06-29.pdf). Data not included in classification. The variant was observed in 1 independent UK families undergoing clinical diagnostic testing, the denominator of which dataset of clinical testing was 16,600. Case control comparison against ethnically matched population data (1/16,600 in familial cases against 0/63,369 GNOMAD NFE controls) pexact= 0.21 2 additional families of Icelandic origin have been tested in the UK. Further cases in Wappenschmidt, B. et al., 2012 PLoS One 7(12): e50800) and Janavicius, R. 2010, EPMA 1(3):397. 5 cases in BIC. 8 reports on ClinVar. The variant is absent in the remainder of the GNOMAD populations (75,263 individuals, but no Icelanders included). Comment. This is a +3 splicing variant which results in alternative splicing but seemingly the impact is mitigated through rescue by alternative functional transcripts. Repeatedly reported in HBOC case, this would appear to be an Icelandic variant; the Icelandic population frequency of this variant is however lacking. The data against segregation and report of a well-phenotyped healthy 58y-old Danish homozygote support this variant being of appreciable population frequency and non-pathogenic. -
Uncertain significance, criteria provided, single submitter	clinical testing	Invitae	Sep 20, 2022	This sequence change falls in intron 10 of the BRCA1 gene. It does not directly change the encoded amino acid sequence of the BRCA1 protein. It affects a nucleotide within the consensus splice site. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with breast cancer and/or ovarian cancer (PMID: 20104584, 23239986, 31683985). It has also been observed to segregate with disease in related individuals. This variant has been observed to be homozygous or hemizygous in an individual who did not have the expected clinical features for that genetic result (PMID: 28588830, 31683985). This variant is also known as IVS11+3A>G. ClinVar contains an entry for this variant (Variation ID: 37566). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown this variant is associated with skipping of exon 10, and a shortened in-frame splice variant that removes a portion of this exon (Δ10q), but one or more of the resulting mRNA isoform(s) may be naturally occurring (PMID: 8972225, 11359908, 11431698, 16943438, 23239986). 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. -

Breast and/or ovarian cancer Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Foulkes Cancer Genetics LDI, Lady Davis Institute for Medical Research

Apr 13, 2013

- -

Familial cancer of breast;C2676676:Breast-ovarian cancer, familial, susceptibility to, 1;C3280442:Pancreatic cancer, susceptibility to, 4;C4554406:Fanconi anemia, complementation group S Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Oct 31, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.025	T
BayesDel_noAF	Benign	-0.27
Cadd	Benign	21
Dann	Benign	0.97
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Benign	0.34	T
MetaRNN	Benign	0.41	T
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D
Sift4G	Benign	1.0	T
Polyphen		0.95	P
Vest4		0.46
MVP		0.85
GERP RS		5.3

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.95
SpliceAI score (max)		0.64		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.64		Position offset: 3

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

Publications

LitVar

Other links and lift over

dbSNP: rs80358015; hg19: chr17-41243449;