[2024-10-21] - Minor: Updated nomenclature for stop codons for oncoKB.

[2024-06-28]

• gnomAD is now 4.1
• Attempt to fix concurrency bug

[2024-06-06] - Minor: we added an additional variant class to the traditionnal 5 AMCG classes. Risk factor can be used to describes variants with decreased penetrance for Mendelian condition. Thanks to Klara Müller for the suggestion.

[2024-03-27] - Bug fix : in some cases (overlapping transcripts), a bug could prevent MobiDetails from retrieving the correct spliceAI values. The spliceAI 500 and spliceAI-visual scores were not concerned by the bug.

[2024-03-26] - New tool : Integration of GeneBe for semi-automated ACMG classifications. Thanks to Piotr Stawiński for giving us the authorisation to include GeneBe ACMG computation in MobiDetails.

[2024-01-18] - Modified MORFEE color code.

[2023-12-22] - RNA HGVS nomenclature is now searched in LOVD and displayed when available in the nomenclature table.

[2023-12-22] - New dataset : MORFEE (Mutation on Open Reading FramE annotation) is a tool that detects and annotates single nucleotide variants (SNVs)

• creating canonical (ATG) and non-canonical Translation Initiation Sites (TIS)
• creating Stop codons (TAA, TAG and TGA)
• deleting Stop codons

in the 5’UTR (uTIS, uStop and New_uStop), the coding sequence (CDS, intTIS, intStop and New_intStop), and the 3’UTR (dTIS, dStop and New_dStop). MORFEE is an R package that could be applied on any VCF file. MORFEE has been applied to all possible SNVs, in the 5’UTR of ~18,000 genes. This so called in silico mutational saturation analysis led to the identification of more than 19,000,000 variations that could alter upORFs constituting the MORFEEdb. MORFEEdb is now available in MobiDetails. A manuscript describing MORFEEdb and its output will be soon made publicly available. For any information related to MORFEEdb output, please contact .

[2023-11-06] - Minor: New link : added direct link gnomAD v4 browser.

[2023-09-21] - New predictor : Integration of AlphaMissense predictions.

[2023-08-18] - Charles redesigned the Homepage.

[2023-07-28] - fixed bug that prevented users to create a new account.

[2023-07-06]

• bedgraphs for SpliceAI-visual are now bgzipped and indexed with tabix in order to save some disk space on the server. Thanks to Jim Robinson for the essential igv.js and for solving an issue with the flask framework and the bgzipped files
• MobiDetails proposes from now on a direct link to MIZTLI for missense variants 3D interpretation. Thanks to Dr. Blavier for the amazing work! MIZTLI proposes the interpretation of missense variants based on alphaFold models or from structures coming form the PDB. In the coming weeks the direct access should evolve to simplify the interpretation. You can from now on check the doc to learn how to manipulate MIZTLI!

[2023-07-03] - Dataset removed: the gnomAD 211 genome frequencies shown were always empty. The dataset has been removed waiting to find a long-term fix.

[2023-06-14]

• feature update : dbsnp updated from v154 to v156 (github issue #53)
• More comprehensible message for variants lying on non-coding transcripts (issue #52)

[2023-06-12]

• New predictor : Integration of AbSplice scores for substitutions (SNVs)
• Minor: nomenclatures fields can now be copied using a button, see discussion #47
• Minor: In addition, issue #42 has been fixed
• Development and Staging versions are now visually identified with different colors in the navigation bar
• added SweetAlert2 explanation and confirmation pop-ups when modifying favourite and clinvar watch lists (authenticated users)
• Integration of a second internal server for VariantValidator. The policy is:
  • CLI calls directed to internal server 1 - if unavailable to internal server 2, if unavailable to the genuine English server
  • Web UI calls directed to internal server 2 - if unavailable to internal server 1, if unavailable to the genuine English server
  The goal is to avoid concurrent queries, and limit this issue which currently occurs on a daily basis.

[2023-03-31] - New feature : Authenticated (logged-in) users can now mark the variants as 'to be added in their ClinVar watch list'. More on this.

[2023-03-19] - New dataset : The REVEL scores are no longer retrieved from dbNSFP, but directly from the REVEL pre-computed dataset. When the hg38 position is not present in the dataset, MobiDetails checks the hg19 one.

[2023-03-03] - New feature : Mobidetails now live queries the ClinGen Evidence Repository and displays the corresponding ACMG classification just below the ClinVar results (to date 4706 curated variants in 81 genes).

[2022-12-19] - feature update : gnomad v3.0 becomes v3.1.2.

[2022-12-21] - New links : Links to OncoKB and CancerVar for genes recognised as oncogenes or tumor suppressor by OncoKB. Added also OncoKB info in gene page and link in gene redirection modal.

[2022-12-19] - New feature : gnomADv2 displays non cancer Max MAF + gnomad v2.0.1 becomes v2.1.1.

[2022-12-19] - New feature : An igv.js browser is now displayed in the gene page, together with the SpliceAI-visual predictions for the canonical transcript.

[2022-12-07] - Minor : Updated SpliceAI-visual rendering for duplications and also for complex indels in strand -.

[2022-11-16] - Minor : Intervar is now queried in hg38 version, which makes it available for hg38_secure trancripts.

[2022-10-27] - New dataset : dbNSFP has been updated from v4.1 to v4.3.

[2022-10-27] - New feature : LitVar has been updated to LitVar2 and the litvar pop-up updated.

[2022-10-27] - New feature : Transcripts that are reported by VariantValidator to poorly match to hg19 are now available for annotation in MobiDetails. Only hg38 linked resources are available. In addition, 43 genes and 3900+ transcripts have been unlocked. These transcripts are marked 'hg38 secured' as depending on the localisation of the variant on the transcript, or on the transcript itself, hg19 mapping may succeed or not. hg19 failed variants lack some annotations or links:

• no EVS link
• no intervar link nor section (waiting for an update)
• no Regulome DB link
• no hg19 nomenclatures
• no gnomADv2
• no hg19 defgen export
• no LOVD export on classification

[2022-08-11] - New resource : Added a link to deCAF (deCODE Allele frequency Browser), which displays allelic frequencies from 150,000 UK genomes.

[2022-07-05] - Software and transcript database update : Modification of the database schema et update of the transcript coming from VariantValidator (version vvta_2022_02).

[2022-06-28] - New feature : A full transcript mutant prediction is now available in SpliceAI-visual on demand.

[2022-06-10] - Bug fix : Disabled SpliceAi Lookup button for delins variants as it does not correclty deal with this type of variants.

[2022-06-09] - Bug fix : Intergenic nucleotides were excluded from SpliceAI-visual predictions.

[2022-05-28] - New predictor : Bedgraph tracks representing spliceai raw scores are displayed in an igv.js browser. This functionality called 'SpliceAI-visual' is based on an original idea and code from Jean-Madeleine de Sainte Agathe and has been built in collaboration with him.

[2022-04-28] - Minor : MuPit called only for missense.

[2022-03-18] - Minor : Improved management of some VV warnings.

[2022-03-18] - Major :

• New API endpoint /api/create/vcf_str: generates annotations from a pseudo-VCF nomenclature (VCF string, e.g. 1-216422237-G-A). Can be used in the search engine (hg38 default or genome version can be added in the VCF string, e.g. hg38-1-216422237-G-A). Separator can be ':', '_' or '-'. Genome version supports GRCh37, GRCh38, hg19, hg38, case insensitive.
• Variants lying in these genes cannot (hopefully temporarily) be accessed: C5orf60, LYST, TET2, MICALCL, UROS, SLC26A10, TCP10L2, STAG2, CRYBG3, DNAH17, EFCAB8, TREX1, SLC22A18AS.
• Along with the missense radar chart, the mean normalised scores for the single predictors family (e.g. SIFT) and for the meta-predictors (e.g. REVEL) are displayed.

[2022-03-03] - New data : Data from the ClinGen Specification Registry is now linked in MD. You can find specific links for the relevant genes in the gene pages (redirection modal) and in the corresponding variants pages. This may help you in using expert panels ACMG criteria during the classification process.

[2022-02-14] - Major : Added about 60,000 transcripts following a major update of VariantValidator. In addition, the submission of a variant lying in any of the proposed transcript will not be forced on canonical transcripts anymore. However, if possible, variants annotated on non-canonical transcripts by users will also be mapped on canonical transcripts (both annotations will be available). MD canonical transcript follow in most cases MANE annotations. Database scheme was also updated.

[2021-10-07] - Minor : Added new links to AlphaFold/EBI protein Structure Database to the gene (redirection modal) and variant pages.

[2021-08-09] - New data : Episignature data for 53 KMT2A variants are now available. See this review to learn more about this concept. Thanks to Pr. Lebre who brought the idea of integrating her team's results into MD.

[2021-06-28] - New tool version : SPiP has been updated to v2.1.

[2021-06-21] - several changes around SPiP:

• New value for parameter caller for the /api/variant/ endpoint: Setting caller to 'clispip' will now return the full results including SPiP (takes longer), while using 'cli' will return the results without SPiP (faster). The swagger page has also bee nupdated to reflect this change.
• SPiP results are now cached to be computed only once and enable a faster access the second (and third....) time
• SPiP has been upgraded to v2. v2 is much more computer intensive than v1 (i.e. is slower). Start a Discussion on github if you have any comments!

[2021-06-18] - New predictor : SpliceAi lookup API can be requested with the non-default parameter distance of 500bp for almost all variants (except complex indels). This can be useful to analyse deep intronic variants as well as large dels and dups.

[2021-06-15] - Minor : HGNC gene symbol and ID now appear in the variant nomenclatures table.

[2021-06-08] - Major : New formatting for the pdf export, which now includes charts and pubmed references, as well as other new features.

[2021-06-02] - Minor : SPiP results are now available using the /api/variant/ API endpoint.

[2021-05-26] - Major : New API endpoint /api/variant/: displays variants details as HTML pages or json files.

[2021-01-16] - Minor : New feature : lists of favourite variants can now be modified directly from the user's variants in the profile page.

[2021-04-09] - Major : New feature : authenticatd users are now able to generate lists of variants accessible form unique and permanent URLs from their favourite list of variants. Users can create several lists, delete them, and use the URL to reference the complete list of variants, e.g. in a publication. All this is available from your profile page.

[2021-04-01] - New external link : new link directed to HexoSplice, a tool to predict the impact of a variant on potential splicing regulatory elements. Only for substitutions.

[2021-01-06] - New external link : When a variant maps onto a 3D structure, a new link is displayed in the left panel to access directly MuPIT

[2021-01-04] - Minor : New search engine keyword: 'last' will return all variants annotated during the last 7 days

[2020-12-01] - New predictor : SPiP is now available as a splicing predictor.

[2020-11-23] - Minor : Added a link to PanelApp in the gene page when relevant.

[2020-11-05] - Minor : Updated CADD from v1.5 to v1.6 and added direct links to CADD lookup for substitutions.

[2020-11-04] - Minor : Added detailed Intervar output (ACMG criteria).

[2020-10-08] - Minor :

• API endpoints /api/gene/ and /api/variant/create_g now deal with HGNC IDs in addition to HGNC names.
• LOVD export is based on HGNC IDs instead of HGNC Names.
• Improved retrieval of HGNC aliases and previous symbols via the search engine.

[2020-10-01] - Minor : Added new API end point to check submitted API keys.

[2020-09-29] - Minor : Pubmed links are now sorted and presented by 1st author, year, journal (title on mouseover).

[2020-09-24] - New predictor : Mistic is now available as a missense predictor.

[2020-09-23] - New function : Variants for which an ACMG class is defined are automatically submitted to LOVD. Read more.

[2020-09-07] - New function : Possibility to annotate variants using dbSNP rs ids (API). The search engine can now be used to annotate variants not only to retrieve existing ones, using the following formats:

• NM_206933.2:c.100C>T
• NC_000001.11:g.216422237G>A;USH2A (hg38 only)
• rs772808534

[2020-08-26] - New function : Added a page to upload a text file for batch variant annotation.

[2020-08-18] - New predictors :

• Scores for miRNA binding predictors miRanda, TargetScan and RNAHybrid from dbMTS have been added for 3'UTR variants.
• Eigen scores have been added, either from dbNSFP for coding variants, or from dbMTS for 3' UTR variants.

[2020-08-14] - Feature update : LOVD effects are now reported when available. LOVD and Intervar results now appear in pdf reports.

[2020-08-12] - Minor: added CSS loader to most pages to increase the browsing comfort.

[2020-08-11] - API changes: 3 methods passed from GET to POST - also update create_vars_batch script in MDUtils package.

[2020-08-11] - Minor : improvements to JS/CSS to make MD more responsive (for small screens)

[2020-07-09] - Minor :

• Adapted MaxEntScan for indels > 9bp
• Added link to RegulomeDB when possible
• New reference/tool version table in about page and pdf export

[2020-07-06] - New admin function : added an 'Forgot my password function' and bug fix with MaxEntScan which could lead to a 500 error.

[2020-06-24] - New API functions : ablility to create variants from genomic coordinates and a HGNC gene name. Ability to update a variant's ACMG class.

[2020-06-20] - CFTR-France and MobiDetails are now working together: All variants in CFTR-France have been integrated into MobiDetails!

[2020-05-25] - New predictor : MaxEntScan is now available as a splicing predictor.

[2020-05-13] - Minor : LOVD instances are now identified by their names when available.

[2020-05-07] - Minor : Registering now requires an email activation.

[2020-04-23] - New predictor :

• Added ClinPred as a new missense predictor (paper).
• Some minor style changes