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Documents, publications and ontologies
ACMG Standards and Guidelines for the Interpretation of Sequence VariantsA Joint Consensus Recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology
Genet Med. 2015 May; 17(5): 405–424.
Copyright © ACGS /VGKL 2013 Practice Guidelines for the Evaluation of Pathogenicity and the Reporting of Sequence Variants in Clinical Molecular Genetics.
HPO Human Phenotype OntologyAn ontology is a computational representation of a domain of knowledgebased upon a controlled, standardized vocabulary for describing entities and the semantic relationships between them. The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Terms in the HPO describes a phenotypic abnormality, such as atrial septal defect.
The HPO was initially developed using information from Online Mendelian Inheritance in Man (OMIM), which is a hugely important data resource in the field of human genetics and beyond. The HPO is currently being developed using information from OMIM and the medical literature and contains approximately 10,000 terms. Over 50,000 annotations to hereditary diseases are available for download or can be browsed using the PhenExplorer.
Clinical scientists assessing these genetic variations routinely use a number of different resources to interpret the mutations and their influence on disease. A number of in silico tools have been developed for assessing the impact of variants on the structure and function of the encoded protein as well as correct splicing. NGRL Manchester aims to provide information about the tools available and guidance on their appropriate use in clinical diagnostics.
Splice prediction tools
Splice Site Tools, a Comparative analysis reportNGRL, Beth Hellen, 2009
Alternative Splice Site Predictor (ASSP)ASSP predicts putative alternative exon isoform, cryptic, and constitutive splice sites of internal (coding) exons. Skipped splice sites are not differentiated from constitutive sites. Non-canonical splice sites are not detected. Alternative splicing is predicted based on the DNA/RNA sequence information only. For splice site prediction within a sequence putative splice sites are preprocessed using position specific score matrices.
ESEfinder: Exonic Splicing Enhancers finderAnalyzes the exonic sequence to find the presence of Exonic Splicing Enhancer Elements.
EX-SKIPEX-SKIP is simple utility that compares the ESE/ESS profile of a wild-type and a mutated allele to quickly determine which exonic variant has the highest chance to skip this exon. It calculates the total number of ESSs, ESEs and their ratio. Specifically, it computes the number of RESCUE-ESEs (Fairbrother 2004; Fairbrother 2002), FAS-ESSs (Wang 2004), PESEs/PESSs (Zhang 2004), neighbourhood inference (Stadler 2006) and EIE/IIEs (Zhang 2008) for each segment.
Fruit Fly Splice PredictorFruit fly and human splice predictor.
GeneSplicerA fast, flexible system for detecting splice sites in the genomic DNA of various eukaryotes. The system has been trained and tested successfully on Plasmodium falciparum (malaria), Arabidopsis thaliana, human, Drosophila, and rice . Training data sets for human and Arabidopsis thaliana are included. See below for instructions on downloading the complete system including source code.
MaxEntScan: predicting splice sites using 'Maximum Entropy Principle'MaxEntScan is based on the approach for modeling the sequences of short sequence motifs such as those involved in RNA splicing which simultaneously accounts for non-adjacent as well as adjacent dependencies between positions. This method is based on the 'Maximum Entropy Principle' and generalizes most previous probabilistic models of sequence motifs such as weight matrix models and inhomogeneous Markov models.
MIT splice predictorGENSCAN Web Server at MIT: identification of complete gene structures in genomic DNA.
RESCUE-ESE: online tool for identifying candidate ESEs in vertebrate exonsSpecific short oligonucleotide sequences that enhance pre-mRNA splicing when present in exons, termed exonic splicing enhancers (ESEs), play important roles in constitutive and alternative splicing (ESE References). A hybrid computational/experimental method, RESCUE-ESE, was recently developed for identifying sequences with ESE activity. In this approach, specific hexanucleotide sequences are identified as candidate ESEs on the basis that they have both significantly higher frequency of occurrence in exons than in introns and also significantly higher frequency in exons with weak (non-consensus) splice sites than in exons with strong (consensus) splice sites. Representative hexamers from ten different classes of candidate ESEs, together with 6 or 7 bases of flanking sequence context on each side, were introduced into a weak (poorly spliced) exon in a splicing reporter construct. These reporter minigenes were then transfected into cultured cells, where they are transcribed and spliced, and the relative level of inclusion of the test exon was assayed by quantitative (radio-labeled) RT-PCR. Point mutants of these sequences were also analyzed to confirm the precise motifs responsible for ESE activity.
Splice Predictor (DK)Splice Predictor (DK)
SplicePort: An Interactive Splice Site Analysis ToolSplicePort is a web-based tool for splice-site analysis that allows the user to make splice-site predictions for submitted sequences. In addition, the user can also browse the rich catalog of features that underlies these predictions, and which we (the authors) have found capable of providing high classification accuracy on human splice sites. Feature selection is optimized for human splice sites, but the selected features are likely to be predictive for other mammals as well.
Various prediction tools
Bio.Tools The use of bioinformatics is ubiquitous within the life sciences. In bio.tools, we are striving to provide a comprehensive registry of software and databases, facilitating researchers from across the spectrum of biological and biomedical science to find, understand, utilise and cite the resources they need in their day-to-day work.
Everything from simple command-line tools and online services, through to databases and complex, multi-functional analysis workflows is included. Resources are described in a rigorous semantics and syntax, providing end-users with the convenience of concise, consistent and therefore comparable information.
Analysis and Quality Control,Phylogenetics, Alignment and sequence manipulation, Immunology, Database search interfaces, Format and display,...
Align-GVGDAlign-GVGD is a freely available, web-based program that combines the biophysical characteristics of amino acids and protein multiple sequence alignments to predict where missense substitutions in genes of interest fall in a spectrum from enriched delterious to enriched neutral. Align-GVGD is an extension of the original Grantham difference to multiple sequence alignments and true simultaneous multiple comparisons.
BLAT Search GenomeBLAT quickly maps your sequence to the genome.
Directly callable from our sequencing software Gensearch.
TraceHaplotyper
This program genotypes a tracefile that results from sequencing of two chromosomes, which one of them having a deletion preceding a SNP. In such case the phase of these markers can be determined.
Shift Detector
This program checks for the possibility that a tracefile results from sequencing of two similar sequences, which one of them having a deletion of 1 to 25 bases. Such deletion would produce a superimposed tracefile following the site of deletion
Online tool developped by Charles University, Prague, to analyse MLPA data. Please ignore the certificate error message. The eMLPA web system performs processing and computational analysis of MLPA data from genetic analyzers (raw data).
eMLPA is a universal user interface for various types of MLPA kits. It offers variant methods of eMLPA data normalization and analysis. No local program installation is needed for analyses – the only pre-requisite is access to the Internet.
To aid our variant interpretation process, we created an openly-available online tool to efficiently classify variants based on the evidence categories outlined in the article: Richards, et al. Standards and guidelines for the interpretation of sequence variants. 2015. This site displays the evidence categories and descriptions from Table 3 and Table 4 with simple checkboxes for selecting appropriate criteria. The site then incorporates the algorithm in Table 5 to automatically assign the pathogenicity or benign impact based on the selected evidence categories.
HansaHansa is a tool to predict the deleterious effects of a mutation by using 10 Neutral- Disease Mis-Sense Mutation Discriminatory (NDMSMD) features. This tool will classify the mutation either as “DISEASE” or “NEUTRAL”
In Silico PCRIn-Silico PCR searches a sequence database with a pair of PCR primers, using an indexing strategy for fast performance.
Mutalyzer HGVS nomenclature checkerThe aim of this program suite is to support checks of sequence variant nomenclature according to the guidelines of the Human Genome Variation Society.
MutationTasterMutationTaster evaluates disease-causing potential of sequence alterations.
PANTHER PSECEstimates the likelihood of a particular nonsynonymous (amino-acid changing) coding SNP to cause a functional impact on the protein. It calculates the subPSEC (substitution position-specific evolutionary conservation) score based on an alignment of evolutionarily related proteins, as described in Thomas et al., 2003 and Thomas & Kejariwal, 2004.
PMUT – Pathogenic mutation predictionPmut is a software aimed at the annotation and prediction of pathological mutations, and in particular at answering the following question: given a mutation happening at a specific location in a protein sequence, can we say whether it will be pathological (that is, a mutation that can lead to disease for the carrier) or non-pathological/neutral (no effect on the carrier's health)? Pmut is based on the use of different kinds of sequence information to label mutations, and neural networks to process this information (Ferrer-Costa et al., 2004). It provides a very simple output: a yes/no answer and a reliability index
PolyPhen2PolyPhen-2 (Polymorphism Phenotyping v2) is a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations. Please, use the form below to submit your query.
Predict ProteinPredictProtein integrates feature prediction for secondary structure, solvent accessibility, transmembrane helices, globular regions, coiled-coil regions, structural switch regions, B-values, disorder regions, intra-residue contacts, protein-protein and protein-DNA binding sites, sub-cellular localization, domain boundaries, beta-barrels, cysteine bonds, metal binding sites and disulphide bridges.
SIFTSIFT predicts whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations.
SNPs3DSNPs3D is a website which assigns molecular functional effects of non-synonymous SNPs based on structure and sequence analysis.
TopoSNPStitziel N O, Binkowski T A, Tseng Y Y, Kasif S, Liang J. 2004. topoSNP: a topographic database of non‐synonymous single nucleotide polymorphisms with and without known disease association. Nucleic Acids Research. 32(suppl_1), D520-D522.
VariantValidator nomenclature checker We validate HGVS sequence variation descriptions, accurately mapping between transcript and genomic variants. We also automate conversion of genomic (VCF) sequence variation descriptions into the HGVS format and vice-versa.
VariantValidator auto-corrects your mistakes if it can and helps you correct your own if it can't. We provide a range of tools to meet your needs including batch processing, a VCF file converter and API access.
Bioinformatics tools for HIV
Geno2pheno [coreceptor] 2.5On submitting a sequence containing the V3 region of the HIV-1 envelope protein gp120 below, you will obtain a sequence alignment to the consensus sequence given in Pfeifer and Lengauer and a prediction whether the corresponding virus is capable of using CXCR4 as a coreceptor (R5/X4 or X4 variants) or not (R5 variants).
HIV BLASTAllows to identify strains of HIV with BLAST.
Directly callable from our HIV sequencing software GensearchHIV.
WebPSSM is a bioinformatic tool for predicting HIV-1 coreceptor usage from the amino acid sequence of the third variable loop (V3) of the envelope gene. Directly callable from our HIV sequencing software GensearchHIV.
Locus specific database software (LSDB)
Cafe Variome Health Data Discovery
Café Variome is a flexible web-based, data discovery tool that can be quickly installed by any biomedical data owner to enable the “existence” rather than the “substance” of the data to be discovered.
LOVD is the software powering the largest network of curated gene variant databases in the world. Directly callable from our software Gensearch.
UMDIt was developed as a generic software to create locus-specific databases (LSDBs) with the 4th Dimension® package from 4D. The UMD software includes an optimized structure to assist and secure data entry and to allow the input of a wide range of clinical data. In addition various analyzing tools have been specifically designed to assist clinicians (phenotype-genotype correlations...), geneticists (distribution and frequency of mutations...) and research biologists (structural domains, molecular epidemiology...).
NGS tools
ExomiserThe Exomiser is a Java program that functionally annotates variants from whole-exome sequencing data in VCF 4 format. The functional annotation is performed with Jannovar and uses UCSC KnownGene transcript definitions and hg19 genomic coordinates.
LIRICALThis application performs phenotype-driven prioritization of candidate diseases and genes in the setting of genomic diagnostics (exome or genome) in which the phenotypic abnormalities are described as Human Phenotype Ontology (HPO) terms.
FastQCFastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.
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Privacy Policy
Last updated: April 21, 2021
This Privacy Policy describes Our policies and procedures on the collection, use and disclosure of Your information when You use the Service and tells You about Your privacy rights and how the law protects You.
We use Your Personal data to provide and improve the Service. By using the Service, You agree to the collection and use of information in accordance with this Privacy Policy. This Privacy Policy has been created with the help of the Privacy Policy Generator.
Interpretation and Definitions
Interpretation
The words of which the initial letter is capitalized have meanings defined under the following conditions. The following definitions shall have the same meaning regardless of whether they appear in singular or in plural.
Definitions
For the purposes of this Privacy Policy:
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Account means a unique account created for You to access our Service or parts of our Service.
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Company (referred to as either "the Company", "We", "Us" or "Our" in this Agreement) refers to Phenosystems SA, 137 Rue de Tubize, 1440 Braine-le-Chateau, Belgium.
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Cookies are small files that are placed on Your computer, mobile device or any other device by a website, containing the details of Your browsing history on that website among its many uses.
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Country refers to: Belgium
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Device means any device that can access the Service such as a computer, a cellphone or a digital tablet.
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Personal Data is any information that relates to an identified or identifiable individual.
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Service refers to the Website.
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Service Provider means any natural or legal person who processes the data on behalf of the Company. It refers to third-party companies or individuals employed by the Company to facilitate the Service, to provide the Service on behalf of the Company, to perform services related to the Service or to assist the Company in analyzing how the Service is used.
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Third-party Social Media Service refers to any website or any social network website through which a User can log in or create an account to use the Service.
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Usage Data refers to data collected automatically, either generated by the use of the Service or from the Service infrastructure itself (for example, the duration of a page visit).
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Website refers to Phenosystems SA, accessible from www.phenosystems.com
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You means the individual accessing or using the Service, or the company, or other legal entity on behalf of which such individual is accessing or using the Service, as applicable.
Collecting and Using Your Personal Data
Types of Data Collected
Personal Data
While using Our Service, We may ask You to provide Us with certain personally identifiable information that can be used to contact or identify You. Personally identifiable information may include, but is not limited to:
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Email address
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Usage Data
Usage Data
Usage Data is collected automatically when using the Service.
Usage Data may include information such as Your Device's Internet Protocol address (e.g. IP address), browser type, browser version, the pages of our Service that You visit, the time and date of Your visit, the time spent on those pages, unique device identifiers and other diagnostic data.
When You access the Service by or through a mobile device, We may collect certain information automatically, including, but not limited to, the type of mobile device You use, Your mobile device unique ID, the IP address of Your mobile device, Your mobile operating system, the type of mobile Internet browser You use, unique device identifiers and other diagnostic data.
We may also collect information that Your browser sends whenever You visit our Service or when You access the Service by or through a mobile device.
Information from Third-Party Social Media Services
The Company allows You to create an account and log in to use the Service through the following Third-party Social Media Services:
If You decide to register through or otherwise grant us access to a Third-Party Social Media Service, We may collect Personal data that is already associated with Your Third-Party Social Media Service's account, such as Your name, Your email address, Your activities or Your contact list associated with that account.
You may also have the option of sharing additional information with the Company through Your Third-Party Social Media Service's account. If You choose to provide such information and Personal Data, during registration or otherwise, You are giving the Company permission to use, share, and store it in a manner consistent with this Privacy Policy.
Tracking Technologies and Cookies
We use Cookies and similar tracking technologies to track the activity on Our Service and store certain information. Tracking technologies used are beacons, tags, and scripts to collect and track information and to improve and analyze Our Service. The technologies We use may include:
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Cookies can be "Persistent" or "Session" Cookies. Persistent Cookies remain on Your personal computer or mobile device when You go offline, while Session Cookies are deleted as soon as You close Your web browser. Learn more about cookies: What Are Cookies?.
We use both Session and Persistent Cookies for the purposes set out below:
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Necessary / Essential Cookies
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Administered by: Us
Purpose: These Cookies are essential to provide You with services available through the Website and to enable You to use some of its features. They help to authenticate users and prevent fraudulent use of user accounts. Without these Cookies, the services that You have asked for cannot be provided, and We only use these Cookies to provide You with those services.
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Cookies Policy / Notice Acceptance Cookies
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Functionality Cookies
Type: Persistent Cookies
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Purpose: These Cookies allow us to remember choices You make when You use the Website, such as remembering your login details or language preference. The purpose of these Cookies is to provide You with a more personal experience and to avoid You having to re-enter your preferences every time You use the Website.
For more information about the cookies we use and your choices regarding cookies, please visit our Cookies Policy or the Cookies section of our Privacy Policy.
Use of Your Personal Data
The Company may use Personal Data for the following purposes:
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To provide and maintain our Service, including to monitor the usage of our Service.
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To manage Your Account: to manage Your registration as a user of the Service. The Personal Data You provide can give You access to different functionalities of the Service that are available to You as a registered user.
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For the performance of a contract: the development, compliance and undertaking of the purchase contract for the products, items or services You have purchased or of any other contract with Us through the Service.
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To contact You: To contact You by email, telephone calls, SMS, or other equivalent forms of electronic communication, such as a mobile application's push notifications regarding updates or informative communications related to the functionalities, products or contracted services, including the security updates, when necessary or reasonable for their implementation.
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To provide You with news, special offers and general information about other goods, services and events which we offer that are similar to those that you have already purchased or enquired about unless You have opted not to receive such information.
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To manage Your requests: To attend and manage Your requests to Us.
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For business transfers: We may use Your information to evaluate or conduct a merger, divestiture, restructuring, reorganization, dissolution, or other sale or transfer of some or all of Our assets, whether as a going concern or as part of bankruptcy, liquidation, or similar proceeding, in which Personal Data held by Us about our Service users is among the assets transferred.
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For other purposes: We may use Your information for other purposes, such as data analysis, identifying usage trends, determining the effectiveness of our promotional campaigns and to evaluate and improve our Service, products, services, marketing and your experience.
We may share Your personal information in the following situations:
- With Service Providers: We may share Your personal information with Service Providers to monitor and analyze the use of our Service, to contact You.
- For business transfers: We may share or transfer Your personal information in connection with, or during negotiations of, any merger, sale of Company assets, financing, or acquisition of all or a portion of Our business to another company.
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- With business partners: We may share Your information with Our business partners to offer You certain products, services or promotions.
- With other users: when You share personal information or otherwise interact in the public areas with other users, such information may be viewed by all users and may be publicly distributed outside. If You interact with other users or register through a Third-Party Social Media Service, Your contacts on the Third-Party Social Media Service may see Your name, profile, pictures and description of Your activity. Similarly, other users will be able to view descriptions of Your activity, communicate with You and view Your profile.
- With Your consent: We may disclose Your personal information for any other purpose with Your consent.
Retention of Your Personal Data
The Company will retain Your Personal Data only for as long as is necessary for the purposes set out in this Privacy Policy. We will retain and use Your Personal Data to the extent necessary to comply with our legal obligations (for example, if we are required to retain your data to comply with applicable laws), resolve disputes, and enforce our legal agreements and policies.
The Company will also retain Usage Data for internal analysis purposes. Usage Data is generally retained for a shorter period of time, except when this data is used to strengthen the security or to improve the functionality of Our Service, or We are legally obligated to retain this data for longer time periods.
Transfer of Your Personal Data
Your information, including Personal Data, is processed at the Company's operating offices and in any other places where the parties involved in the processing are located. It means that this information may be transferred to — and maintained on — computers located outside of Your state, province, country or other governmental jurisdiction where the data protection laws may differ than those from Your jurisdiction.
Your consent to this Privacy Policy followed by Your submission of such information represents Your agreement to that transfer.
The Company will take all steps reasonably necessary to ensure that Your data is treated securely and in accordance with this Privacy Policy and no transfer of Your Personal Data will take place to an organization or a country unless there are adequate controls in place including the security of Your data and other personal information.
Disclosure of Your Personal Data
Business Transactions
If the Company is involved in a merger, acquisition or asset sale, Your Personal Data may be transferred. We will provide notice before Your Personal Data is transferred and becomes subject to a different Privacy Policy.
Law enforcement
Under certain circumstances, the Company may be required to disclose Your Personal Data if required to do so by law or in response to valid requests by public authorities (e.g. a court or a government agency).
Other legal requirements
The Company may disclose Your Personal Data in the good faith belief that such action is necessary to:
- Comply with a legal obligation
- Protect and defend the rights or property of the Company
- Prevent or investigate possible wrongdoing in connection with the Service
- Protect the personal safety of Users of the Service or the public
- Protect against legal liability
Security of Your Personal Data
The security of Your Personal Data is important to Us, but remember that no method of transmission over the Internet, or method of electronic storage is 100% secure. While We strive to use commercially acceptable means to protect Your Personal Data, We cannot guarantee its absolute security.
Children's Privacy
Our Service does not address anyone under the age of 13. We do not knowingly collect personally identifiable information from anyone under the age of 13. If You are a parent or guardian and You are aware that Your child has provided Us with Personal Data, please contact Us. If We become aware that We have collected Personal Data from anyone under the age of 13 without verification of parental consent, We take steps to remove that information from Our servers.
If We need to rely on consent as a legal basis for processing Your information and Your country requires consent from a parent, We may require Your parent's consent before We collect and use that information.
Links to Other Websites
Our Service may contain links to other websites that are not operated by Us. If You click on a third party link, You will be directed to that third party's site. We strongly advise You to review the Privacy Policy of every site You visit.
We have no control over and assume no responsibility for the content, privacy policies or practices of any third party sites or services.
Changes to this Privacy Policy
We may update Our Privacy Policy from time to time. We will notify You of any changes by posting the new Privacy Policy on this page.
We will let You know via email and/or a prominent notice on Our Service, prior to the change becoming effective and update the "Last updated" date at the top of this Privacy Policy.
You are advised to review this Privacy Policy periodically for any changes. Changes to this Privacy Policy are effective when they are posted on this page.
Contact Us
If you have any questions about this Privacy Policy, You can contact us:
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