rs28897696
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM1PM5PP3
The NM_007294.4(BRCA1):c.5123C>T(p.Ala1708Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000198 in 1,613,780 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A1708E) has been classified as Pathogenic.
Frequency
Genomes: 𝑓 0.000072 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000014 ( 0 hom. )
Consequence
BRCA1
NM_007294.4 missense
NM_007294.4 missense
Scores
12
3
2
Clinical Significance
Conservation
PhyloP100: 6.18
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 5 ACMG points.
PM1
?
In a hotspot region, there are 10 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 5 benign, 16 uncertain in NM_007294.4
PM5
?
Other missense variant is known to change same aminoacid residue: Variant chr17-43063903-G-T is described in ClinVar as [Pathogenic]. Clinvar id is 55407.Status of the report is reviewed_by_expert_panel, 3 stars.
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.79
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| BRCA1 | NM_007294.4 | c.5123C>T | p.Ala1708Val | missense_variant | 17/23 | ENST00000357654.9 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| BRCA1 | ENST00000357654.9 | c.5123C>T | p.Ala1708Val | missense_variant | 17/23 | 1 | NM_007294.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152096Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251312Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135846
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:19Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Breast-ovarian cancer, familial, susceptibility to, 1 Uncertain:6Other:1
| Uncertain significance, no assertion criteria provided | clinical testing | Department of Medical Genetics, University Hospital of North Norway | May 01, 2016 | - - |
| Uncertain significance, no assertion criteria provided | clinical testing | BRCAlab, Lund University | Mar 02, 2020 | - - |
| Uncertain significance, no assertion criteria provided | clinical testing | Sharing Clinical Reports Project (SCRP) | May 01, 2012 | - - |
| Uncertain significance, criteria provided, single submitter | clinical testing | Institute of Human Genetics, University of Leipzig Medical Center | Jul 09, 2018 | - - |
| Uncertain significance, criteria provided, single submitter | clinical testing | All of Us Research Program, National Institutes of Health | Nov 20, 2023 | This missense variant replaces alanine with valine at codon 1708 of the BRCA1 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Functional studies have reported conflicting findings on the activity of the variant protein on various in vitro and ex vivo assays (PMID: 18036263, 20516115, 26689913, 30209399, 30458859). This variant has been reported in individuals with personal and/or family history of breast or ovarian cancer (PMID: 15744030, 16489001, 17403394, 22034289, 26287763, 27495310) including individuals who also had a BRCA2 pathogenic co-variant (PMID: 15744030, 17403394) and in healthy controls (PMID: 15744030, 24055113, 25637381). This variant has also been reported in an individual affected with kidney renal clear cell carcinoma (PMID: 26689913). A different variant affecting the same codon (p.Ala1708Glu) is considered to be disease-causing (ClinVar variation ID: 55407), suggesting that alanine or similar amino acid at this position is important for the protein function. This variant has been identified in 8/282694 chromosomes 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 | Baylor Genetics | Oct 24, 2023 | - - |
| not provided, no classification provided | in vitro | Brotman Baty Institute, University of Washington | - | - - |
not specified Uncertain:3
| Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jun 09, 2020 | DNA sequence analysis of the BRCA1 gene demonstrated a sequence change, c.5123C>T, in exon 17 that results in an amino acid change, p.Ala1708Val. This sequence change has been described in patients with a personal and/or family history of breast cancer, as well as in control populations undergoing exome sequencing (PMIDs: 25637381, 24055113). PMID 20516115 demonstrated a severe folding defect and compromised binding activity and binding specificity associated with the p.Ala1708Val change. However, PMID 18036263 demonstrated an intermediate effect on transcriptional transactivation associated with the p.Ala1708Val change, more suggestive of a low or moderate risk allele. This sequence change has been described in the gnomAD database with a low population frequency of 0.03% (dbSNP rs28897696). The p.Ala1708Val change affects a highly conserved amino acid residue located in a domain of the BRCA1 protein that is known to be functional. The p.Ala1708Val substitution appears to be deleterious using several in-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL). Due to these contrasting evidences and the lack of functional studies, the clinical significance of the p.Ala1708Val change remains unknown at this time. - |
| Uncertain significance, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Dec 28, 2023 | Variant summary: BRCA1 c.5123C>T (p.Ala1708Val) results in a non-conservative amino acid change located in the BRCT domain (IPR001357) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 2.8e-05 in 251672 control chromosomes (gnomAD). Another BRCA1 missense change at the same residue p.Ala1708Glu (c.5123C>A) is a known pathogenic variant. It must be noted that while p.Ala1708Glu leads to change in amino acid charge (neutral to polar), this variant, (p.Ala1708Val) does not. c.5123C>T has been reported in the literature in individuals affected with breast and/or ovarian and other cancers (example: Caldes_2002, Chenevix-Trench_2006, Lovelock_2007, Fackenthal_2012, Lu_2015, Pal_2015, Jarhelle_2016, Moller_2019, Zhang_2022, Yang_2022). These reports do not provide unequivocal conclusions about association of the variant with Hereditary Breast And Ovarian Cancer Syndrome. This variant was also reported in the FLOSSIES database in women older than age 70 years who have never had cancer. Co-occurrences with pathogenic BRCA2 variants have been observed at our laboratory (c.5641_5644delAAAT, p.Lys1881GlnfsX27; c.8188G>C, p.Ala2730Pro; c.3939_3943delCAAGA, p.Y1313X), while an additional non-specified BRCA2 co-occurrence has been reported by an external laboratory in the ClinVar database (SCV000076816.10), providing supporting evidence for a benign role. Multiple publications have reported experimental evidence evaluating an impact on protein function. The most pronounced variant effect leads to varied outcomes depending upon types of assays performed (example, Lovelock_2007, Lee_2008, Lu_2015, Findlay_2018, Fernandes_2019, Petitalot_2019, Bassi_2023). The variant had normal effect on protein expression and foci formation in response to DNA damage, functional homology directed repair (HDR) activity, but had conflicting results ranging from normal to intermediate/strong effect on transcription, protein folding, centrosome amplification and phosphopeptide binding. For these reasons, a recent study reports this variant among those having an intermediate impact (Petitalot_2019). The possibility of the variant being a hypomorphic mildly causative allele associated with a late onset/variable penetrance cannot be ruled out. The following publications have been ascertained in the context of this evaluation (PMID: 30263132, 25637381, 12161611, 16489001, 24055113, 22034289, 30765603, 30209399, 21702907, 29625052, 27495310, 30458859, 20516115, 15744030, 18036263, 26689913, 30678073, 26287763, 30257991, 17403394, 22889855, 28781887, 11802208, 35918668, 35918668, 37085799).Ten ClinVar submitters have assessed this variant since 2014: all submitters classified the variant as uncertain significance. Some submitters cite overlapping but not identical evidence utilized in the context of this evaluation. Based on the evidence outlined above, the variant was classified as uncertain significance. - |
| Uncertain significance, no assertion criteria provided | research | Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto | Jan 31, 2014 | - - |
Hereditary cancer-predisposing syndrome Uncertain:3
| Uncertain significance, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Jan 18, 2024 | This missense variant replaces alanine with valine at codon 1708 of the BRCA1 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function. Functional studies have reported conflicting findings on the activity of the variant protein on various in vitro and ex vivo assays (PMID: 18036263, 20516115, 26689913, 30209399, 30458859). This variant has been reported in individuals with personal and/or family history of breast or ovarian cancer (PMID: 15744030, 16489001, 17403394, 22034289, 26287763, 27495310) including individuals who also had a BRCA2 pathogenic co-variant (PMID: 15744030, 17403394) and in healthy controls (PMID: 15744030, 24055113, 25637381). This variant has also been reported in an individual affected with kidney renal clear cell carcinoma (PMID: 26689913). A different variant affecting the same codon (p.Ala1708Glu) is considered to be disease-causing (ClinVar variation ID: 55407), suggesting that alanine or similar amino acid at this position is important for the protein function. This variant has been identified in 8/282694 chromosomes 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 | Apr 26, 2023 | The p.A1708V variant (also known as c.5123C>T), located in coding exon 16 of the BRCA1 gene, results from a C to T substitution at nucleotide position 5123. The alanine at codon 1708 is replaced by valine, an amino acid with similar properties. This alteration impacts the functionally important BRCT domain and has been associated with reduced/partial BRCA1 function, suggesting that p.A1708V may act as a low or moderate disease risk allele (Lu C et al. Nat Commun. 2015 Dec;6:10086; Lee MS et al. Cancer Res. 2010 Jun;70:4880-90; Lovelock PK et al. Breast Cancer Res. 2007;9:R82). Based on one functional study, using saturation genome editing, this alteration does not affect the BRCA1 protein (Findlay GM et al. Nature. 2018 10;562:217-222). Of note, this alteration is also known as 5242C>T in published literature. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence conflicting at this time, the clinical significance of this alteration remains unclear. - |
| Uncertain significance, criteria provided, single submitter | curation | Sema4, Sema4 | Jun 15, 2021 | - - |
not provided Uncertain:2
| Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Sep 26, 2023 | Published functional studies showed mixed results with respect to folding ability, binding activity and specificity, homologous recombination repair activity, transcriptional activation, centrosome amplification, foci formation in response to DNA damage, and cell survival (Lovelock et al., 2007; Lee et al., 2010; Lu et al., 2015; Woods et al., 2016; Findlay et al., 2018; Langerud et al., 2018; Fernandes et al., 2019; Petitalot et al., 2019; Iversen et al., 2022; Bassi et al., 2023); Observed in individuals with a personal and/or family history of breast and other cancers (Chenevix-Trench et al., 2006; Fackenthal et al., 2012; Lu et al., 2015; Pal et al., 2015; Zhang et al., 2022; Rioki et al., 2023); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Also known as 5242C>T; This variant is associated with the following publications: (PMID: 24607278, 22889855, 17403394, 26689913, 26287763, 30263132, 29625052, 16489001, 18036263, 20516115, 22034289, 25637381, 20522429, 15744030, 12161611, 24055113, 28024868, 27720647, 27495310, 28781887, 30209399, 30458859, 30765603, 23867111, 21702907, 15923272, 11802208, 31409081, 30257991, 30678073, 32377563, 25348405, 35665744, 37085799, 35918668, 36451132, 34621001, 37719058, 1157798, 34981296) - |
| Uncertain significance, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Jan 27, 2023 | The frequency of this variant in the general population, 0.00028 (7/24954 chromosomes in African/African American subpopulation, http://gnomad.broadinstitute.org), is higher than would generally be expected for pathogenic variants in this gene. In the published literature, the variant has been reported in individuals affected with breast cancer (PMID: 17403394 (2007), 22034289 (2012), 26287763 (2015), 27495310 (2016), and kidney cancer (PMID: 26689913 (2015), 29625052 (2018)). Assessment of experimental analysis yielded conflicting results regarding the impact of this variant on protein function (PMID: 18036263 (2007), 20516115 (2010), 22889855 (2012), 26689913 (2015), 30209399 (2018), 30458859 (2018), 30257991 (2018)). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, we are unable to determine the clinical significance of this variant. - |
Hereditary breast ovarian cancer syndrome Uncertain:2
| Uncertain significance, criteria provided, single submitter | clinical testing | St. Jude Molecular Pathology, St. Jude Children's Research Hospital | Aug 04, 2021 | - - |
| Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Dec 15, 2023 | This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 1708 of the BRCA1 protein (p.Ala1708Val). This variant is present in population databases (rs28897696, gnomAD 0.03%). This missense change has been observed in individual(s) with a personal and/or family history of breast cancer and/or kidney cancer (PMID: 16489001, 18036263, 22034289, 26287763, 26689913, 27495310). This variant is also known as 5242C>T (A1708V). ClinVar contains an entry for this variant (Variation ID: 37640). Advanced modeling performed at Invitae incorporating data from internal and/or published experimental studies (PMID: 30209399) indicates that this missense variant is not expected to disrupt BRCA1 function with a negative predictive value of 95%. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on BRCA1 function (PMID: 18036263, 20516115, 26689913, 30209399). This variant disrupts the p.Ala1708 amino acid residue in BRCA1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 1157798, 11802208, 15923272, 19404736, 23867111). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. 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 Uncertain:1
| Uncertain significance, no assertion criteria provided | research | CSER _CC_NCGL, University of Washington | Jun 01, 2014 | - - |
Malignant tumor of breast Uncertain:1
| Uncertain significance, no assertion criteria provided | clinical testing | Department of Pathology and Laboratory Medicine, Sinai Health System | - | The BRCA1 p.Ala1708Val variant was identified in 1 of 2000 proband chromosomes (frequency: 0.001) from individuals or families with breast cancer, and was not identified in 180 control chromosomes from healthy individuals (Dorschner 2013); however, an insufficient number of controls were included in these studies to determine the frequency of this variant in the general population. The variant was also identified in dbSNP (ID: rs28897696) “With Pathogenic, Uncertain significance allele”, NHLBI Exome Sequencing Project (Exome Variant Server), Exome Aggregation Consortium (ExAC) database, HGMD, LOVD, the ClinVar database (classified as a uncertain significance variant by the Sharing Clinical Reports Project, derived from Myriad reports; Ambry Genetics; CSER_CC_NCGL and GeneDX), GeneInsight VariantWire database(1X, classified as “unknown significance” by a clinical laboratory) and UMD (2X as a unknown significance variant).This variant was identified in the HAPMAP-JPT in 1 of 168 chromosomes (frequency: 0.006), Exome Variant Server project in 3 of 13006 European American/African American alleles, the Exome Aggregation Consortium (ExAC) database (released Oct 20th, 2014) in 4 of 10284 chromosomes (frequency: 0.0004) from a population of African individuals, although this low number of observations and low frequency is not substantive enough to determine the prevalence of the variant in the general population and its relationship to disease. The p.Ala1708 residue is conserved across mammals and other organisms, and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the p.Ala1708 variant may impact the protein. However, this information is not predictive enough to assume pathogenicity. Functional studies by Chenevix-Trench (2006) and Lee (2010) characterized the variant as unclassified with odds of 41:1 in favor of causality with strong functional effect. In addition, in the study by Lovelock (2007) this variant displayed an intermediate transcriptional transactivation activity and a normal foci formation response in response to DNA damage but induced centrosome amplification. The results of this study also raise the possibility that variant may be associated with a low or moderate risk of cancer. 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 unknown significance. - |
Familial cancer of breast Uncertain:1
| Uncertain significance, no assertion criteria provided | literature only | Center for Precision Medicine, Meizhou People's Hospital | - | - - |
Computational scores
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Name
Calibrated prediction
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AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Pathogenic
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Pathogenic
D;D;D;D;D;D;D;D;D;D;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D;D;D;D;D;D;D;D;D
MetaSVM
Pathogenic
D
MutationTaster
Benign
D;D;D;D;D;D;D;D;D;D;D;D;D;N
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;N;.;D;.;.;N;D;D;N;D
REVEL
Pathogenic
Sift
Benign
D;D;.;D;.;.;D;D;D;D;D
Sift4G
Pathogenic
D;D;D;D;D;D;D;D;.;.;D
Polyphen
1.0, 1.0
.;D;.;.;.;D;.;.;.;D;.
Vest4
MVP
MPC
0.38
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at