17-43091432-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_007294.4(BRCA1):c.4096+3A>G variant causes a splice 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. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★★★).
Frequency
Consequence
NM_007294.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461602Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727064
GnomAD4 genome
ClinVar
Submissions by phenotype
Breast-ovarian cancer, familial, susceptibility to, 1 Pathogenic:3Uncertain:5
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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. -
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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G variant may not exhibit the clinical characteristics of a standard high-risk pathogenic BRCA1 variant (Spurdle, unpublished data).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. -
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not provided Uncertain:3
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) -
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. -
The BRCA1 c.4096+3A>G variant has been reported in the published literature in breast or ovarian cancer cases (PMIDs: 20104584 (2010), 23239986 (2012), 24728189 (2014), 25683334 (2015), 31683985 (2019)), as well as in unaffected individuals in the heterozygous and homozygous state, with non-segregation with disease (PMID: 28588830 (2017)). RNA studies in vitro have shown this variant impaired normal splicing at the neighboring splice junction, resulting in the loss of the full length BRCA1 transcript and an increased abundance of a naturally occurring, shortened in-frame isoform that removes a portion of the largest exon (PMID: 23239986 (2012)). This shortened isoform is expressed in various healthy tissues and may be partially functional (PMIDs: 8972225 (1997), 11359908 (2001), and 24569164 (2014)). This variant has not been reported in large, multi-ethnic general populations (Genome Aggregation Database, http://gnomad.broadinstitute.org). Based on the available information, we are unable to determine the clinical significance of this variant. -
Hereditary breast ovarian cancer syndrome Uncertain:2Benign:1
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 personal and/or family history of breast and/or ovarian cancer (PMID: 20104584, 23239986, 31683985, 31954625, 34981296). It has also been observed to segregate with disease in related individuals. This variant has been observed to be homozygous, hemizygous or homoplasmic 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; Invitae). 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. -
The splice region variant NM_007294.4(BRCA1):c.4096+3A>G has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.4096+3A>G variant is novel (not in any individuals) in gnomAD. The c.4096+3A>G variant is novel (not in any individuals) in 1kG. The c.4096+3A>G variant is predicted to disrupt the existing donor splice site 1bp upstream by 3 of 4 splice site algorithms. For these reasons, this variant has been classified as Uncertain Significance. -
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. -
not specified Uncertain:2
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 the variant abolishes a 5' splicing donor site. However, these predictions have yet to be confirmed by functional studies. A functional study confirms that this variant compromises the existing intron 11 donor splice site, 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 been described, adding to the complexity of assessing the effect of the variant. The variant allele was found at a frequency of 3.7e-06 in 1620956 control chromosomes (gnomAD database v4 and literature). 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 (e.g. 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 year old homozygous female and a 47 year old female with breast cancer who tested negative for this variant (Byrjalsen_2017). The variant was also found in 8 breast cancer probands and numerous family members with other cancer phenotypes in an Icelandic cohort, including a homozygote carrier affected with lung cancer (Arason_2019) without strong evidence for causality. Co-occurrences with other pathogenic variant(s) have been reported (BRCA2 c.7007G>A,, p.Arg2336His; ATM c.6404_6405insTT , p.Arg2136fsX1)(Beissel_ 2014, internal testing), providing supporting evidence for a benign role. The following publications have been ascertained in the context of this evaluation (PMID: 31683985, 26075997, 20104584, 28588830, 17591843, 28195393, 34981296, 23199084, 16267036, 29750258, 26733283, 24728189, 23239986). ClinVar contains an entry for this variant (Variation ID: 37566). Based on the evidence outlined above, the variant was classified as uncertain significance. -
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Hereditary cancer-predisposing syndrome Uncertain:2
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. -
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. -
Breast and/or ovarian cancer Pathogenic:1
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BRCA1-related cancer predisposition Uncertain:1
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. -
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
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at