scout-browser 4.98.0__py3-none-any.whl → 4.100.0__py3-none-any.whl

scout/server/blueprints/cases/templates/cases/case_report.html

@@ -63,7 +63,7 @@
 </nav>
 
 <div id="container" class="container">
-  <h4>Scout case analysis report</h4> - created on:&nbsp;<strong>{{report_created_at}}</strong> using <strong>Scout v.{{current_scout_version}}</strong><br><br>
+  <h4>Scout case analysis report</h4> - created on:&nbsp;<strong>{{report_created_at}}</strong> using <strong>Scout v{{current_scout_version}}</strong> for genome build <strong>{{case.genome_build }}</strong>.<br><br>
    {{ phenotype_panel() }}
    {{ gene_panels_panel()}}
    {{ causatives_panel()}}
@@ -104,7 +104,7 @@
                 <td>Case created: <strong>{{case.created_at.strftime('%Y-%m-%d')}}</strong></td>
 	              <td>Last updated: <strong>{{case.updated_at.strftime('%Y-%m-%d') if case.updated_at else "n.a." }}</strong></td>
                 {% if case.scout_load_version %}
-                  <td> Loaded with <strong>Scout v.{{case.scout_load_version}}</strong></td>
+                  <td> Loaded with <strong>Scout v{{case.scout_load_version}}</strong></td>
                 {% endif %}
 	            </tr>
 	          </table>
@@ -383,7 +383,7 @@
     {% set duplicated_variants = [] %}
     {% if variants.classified_detailed %}
       {% for variant in variants.classified_detailed|sort(attribute='variant_rank') %}
-        {% if variant['_id'] not in printed_vars %}
+        {% if variant['_id'] not in printed_vars and variant not in variants.dismissed_detailed %}
           {% do printed_vars.append(variant['_id']) %}
           {{ variant_content(variant, loop.index) }}
           <br>
@@ -395,7 +395,7 @@
       No ACMG-classified variants available for this case
     {% endif %}
     {% if variants.classified_detailed and duplicated_variants|length == variants.classified_detailed|length %}
-      All ACMG-classified variants are already described in the previous views
+      All ACMG-classified variants are already described in the other panels
     {% endif %}
   </div>
 </div>
@@ -410,7 +410,7 @@
     {% set duplicated_variants = [] %}
     {% if variants.ccv_classified_detailed %}
       {% for variant in variants.ccv_classified_detailed|sort(attribute='variant_rank') %}
-        {% if variant['_id'] not in printed_vars %}
+        {% if variant['_id'] not in printed_vars and variant not in variants.dismissed_detailed %}
           {% do printed_vars.append(variant['_id']) %}
           {{ variant_content(variant, loop.index) }}
           <br>
@@ -422,7 +422,7 @@
       No ClinGen-CGC-VICC-classified variants available for this case
     {% endif %}
     {% if variants.ccv_classified_detailed and duplicated_variants|length == variants.ccv_classified_detailed|length %}
-      All ClinGen-CGC-VICC-classified variants are already described in the previous views
+      All ClinGen-CGC-VICC-classified variants are already described in the other panels
     {% endif %}
   </div>
 </div>
@@ -437,7 +437,7 @@
     {% set duplicated_variants = [] %}
     {% if variants.tagged_detailed %}
       {% for variant in variants.tagged_detailed|sort(attribute='variant_rank') %}
-        {% if variant['_id'] not in printed_vars %}
+        {% if variant['_id'] not in printed_vars and variant not in variants.dismissed_detailed %}
           {% do printed_vars.append(variant['_id']) %}
           {{ variant_content(variant, loop.index) }}
           <br>
@@ -461,7 +461,7 @@
       No tagged variants for this case
     {% endif %}
     {% if (variants.tagged_detailed or variants.tier_detailed) and duplicated_variants|length == (variants.tagged_detailed|length+variants.tier_detailed|length) %}
-      All tagged variants are already described in the previous views
+      All tagged variants are already described in the other panels
     {% endif %}
   </div>
 </div>
@@ -500,7 +500,7 @@
     {% set duplicated_variants = [] %}
     {% if variants.commented_detailed %}
       {% for variant in variants.commented_detailed|sort(attribute='variant_rank') %}
-        {% if variant['_id'] not in printed_vars %}
+        {% if variant['_id'] not in printed_vars and variant not in variants.dismissed_detailed %}
           {% do printed_vars.append(variant['_id']) %}
           {% if variant.category == 'snv' %}
             {{ sn_variant_content(variant, loop.index) }}
@@ -520,7 +520,7 @@
       No commented variants for this case
     {% endif %}
     {% if variants.commented_detailed and duplicated_variants|length == variants.commented_detailed|length %}
-      All commented variants are already described in the previous views
+      All commented variants are already described in the other panels
     {% endif %}
   </div>
 </div>
@@ -845,7 +845,8 @@
                 <th class="w-5"></th>
                 <th class="w-25"><strong>Variant</strong></th>
                 <th class="w-5"><strong>Category</strong></th>
-  	            <th class="w-25"><strong>Genes</strong></th>
+  	            <th class="w-20"><strong>Genes</strong></th>
+                <th class="w-5"><strong>Classification</strong></th>
                 <th class="w-45"><strong>Dismissed description</strong></th>
             </tr>
           </thead>
@@ -867,7 +868,14 @@
               <td style="width:15%;"
                 {{ dismissed_gene_list(variant) }}
               </td>
-
+              <td>
+                {% if variant.acmg_classification %}
+                  <span class="badge rounded-pill bg-{{variant.acmg_classification['color'] if variant.acmg_classification['color'] else 'secondary'}}" title="{{variant.acmg_classification['code']}}">{{variant.acmg_classification['short'] }}</span>
+                {% endif %}
+                {% if variant.ccv_classification %}
+                  <span class="badge rounded-pill bg-{{variant.ccv_classification['color'] if variant.ccv_classification['color'] else 'secondary'}}" title="{{variant.ccv_classification['code']}}">{{variant.ccv_classification['short'] }}</span>
+                {% endif %}
+              </td>
               <td rowspan="2">
                 <ul>
                   {% for reason in variant.dismiss_variant if not reason == "Select a tag"  %}
@@ -1531,7 +1539,11 @@
   <td>
     {% if variant.acmg_classification %}
       <span class="badge rounded-pill bg-{{variant.acmg_classification['color'] if variant.acmg_classification['color'] else 'secondary'}}" title="{{variant.acmg_classification['code']}}">{{variant.acmg_classification['short'] }}</span>
-    {% elif variant.manual_rank %}
+    {% endif %}
+    {% if variant.ccv_classification%}
+      <span class="badge rounded-pill bg-{{variant.ccv_classification['color'] if variant.ccv_classification['color'] else 'secondary'}}" title="{{variant.ccv_classification['code']}}">{{variant.ccv_classification['short'] }}</span>
+    {% endif%}
+    {% if variant.manual_rank %}
       <span class="badge rounded-pill bg-secondary" title="Manual rank">{{ manual_rank_options[variant.manual_rank]['label'] }}</span>
     {% else %}
       -

scout/server/blueprints/cases/templates/cases/chanjo2_form.html

@@ -1,6 +1,6 @@
 {% macro chanjo2_report_form(institute_obj, case_obj, panel_name, report_type, hgnc_ids, link_text, link_class = "link-primary") %}
 
-  {% set form_name = "chanjo2_"+panel_name+"_"+report_type %}
+  {% set form_name = "chanjo2_" ~ panel_name ~ "_" ~ report_type %}
   {% set form_action = config.CHANJO2_URL+"/"+report_type %}
   {% set build = "GRCh38" if "38" in case_obj.get("genome_build", "37") else "GRCh37" %}
   {% set default_level = institute_obj.coverage_cutoff %}

scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html

@@ -196,7 +196,7 @@
   <div href="#" class="bg-dark list-group-item text-white" data-bs-toggle="tooltip" title="Scout version used for loading the case" data-bs-placement="right">
     <div class="d-flex w-100 justify-content-start align-items-center">
       <span class="fa fa-gear fa-fw me-3"></span>
-      <span class="menu-collapsed">v.{{ case.scout_load_version }}</span>
+      <span class="menu-collapsed">v{{ case.scout_load_version }}</span>
     </div>
   </div>
 {% endif %}

scout/server/blueprints/cases/templates/cases/gene_panel.html

@@ -18,7 +18,7 @@
           {% for panel in case.panels %}
             <tr {% if panel.is_default %} class="bg-info" {% endif %}>
               <td>
-                <a {% if panel.is_default %} class="text-white" {% endif %} href="{{ url_for('panels.panel', panel_id=panel.panel_id, case_id=case._id, institute_id=institute._id) }}">
+                <a {% if panel.is_default %} class="text-white" {% endif %} href="{{ url_for('panels.panel', panel_id=panel.panel_id, case_id=case._id, institute_id=institute._id) }}" target="_blank" rel="noopener">
                   {{ panel.display_name|truncate(30, True) }}
                 </a>
                 {% if panel.removed %}

scout/server/blueprints/cases/templates/cases/utils.html

@@ -313,6 +313,22 @@
 
       {{ display_genes|join(", ") }}
 
+    {% elif variant.category == "outlier" %}
+      {{ variant.sub_category|upper }} - {% if variant.genes %}
+        {% for gene in variant.genes %}
+           {% if gene.hgnc_symbol %}
+             {{ gene.hgnc_symbol }}
+           {% else %}
+             {{gene.hgnc_id}}
+           {% endif %}
+        {% endfor %} - {%  if variant.sub_category == "splicing" %}
+          {{ variant.delta_psi }}Δψ  {{ variant.potential_impact }} - fs {{ variant.causes_frameshift }}
+        {% else %}
+          {{ variant.l2fc }}{% if variant.l2fc > 0 %}&uarr;{% elif variant.l2fc < 0 %}&darr;{% endif %}
+        {% endif %}
+      {% else %}
+        {{ variant.gene_name_orig }}
+      {% endif %}
     {% else %} <!-- structural variants -->
       {{ variant.sub_category|upper }}({{ variant.chromosome }}{{ variant.cytoband_start }}-{{ variant.end_chrom }}{{ variant.cytoband_end }})
     {% endif %}
@@ -325,21 +341,24 @@
 
   {% if variant.category in ("mei", "str", "snv", "cancer") %}
     {% if variant.category == "cancer" %}
-    <a href="{{ url_for('variant.cancer_variant',
+    <a href='{{ url_for('variant.cancer_variant',
                    institute_id=variant.institute,
                    case_name=case.display_name,
-                   variant_id=variant._id) }}" target="_blank">
+                   variant_id=variant._id) }}' target='_blank'>
     {% else %}
-    <a href="{{ url_for('variant.variant',
+    <a href='{{ url_for('variant.variant',
                    institute_id=variant.institute,
                    case_name=case.display_name,
-                   variant_id=variant._id) }}" target="_blank">
+                   variant_id=variant._id) }}' target='_blank'>
     {% endif %}
+  {% elif variant.category == "outlier" %}
+    <a href='{{ url_for('omics_variants.outliers',
+       institute_id=variant.institute, case_name=case.display_name) }}' target='_blank'>
   {% else %} <!-- structural variants -->
-    <a href="{{ url_for('variant.sv_variant',
+    <a href='{{ url_for('variant.sv_variant',
                               institute_id=variant.institute,
                               case_name=case.display_name,
-                              variant_id=variant._id) }}" target="_blank">
+                              variant_id=variant._id) }}' target='_blank'>
   {% endif %}
     {{ pretty_variant(variant) }}
   </a>

scout/server/blueprints/clinvar/controllers.py

@@ -28,30 +28,45 @@ LOG = logging.getLogger(__name__)
 
 
 def _get_var_tx_hgvs(case_obj: dict, variant_obj: dict) -> List[Tuple[str, str]]:
-    """Retrieve all transcripts / hgvs for a given variant."""
+    """Retrieve all transcripts / HGVS for a given variant."""
 
     build = str(case_obj.get("genome_build", "37"))
     tx_hgvs_list = [("", "Do not specify")]
+    case_has_build_37 = "37" in case_obj.get("genome_build", "37")
+
     add_gene_info(store, variant_obj, genome_build=build)
+
     for gene in variant_obj.get("genes", []):
-        for tx in gene.get("transcripts", []):
+        transcripts = gene.get("transcripts", [])
+
+        for tx in transcripts:
+
+            refseq_id = tx.get("refseq_id")
+            coding_seq_name = tx.get("coding_sequence_name")
+            if not (refseq_id and coding_seq_name):
+                continue  # Skip transcripts missing required fields
+
             mane_select = tx.get("mane_select_transcript")
-            if all([tx.get("refseq_id"), tx.get("coding_sequence_name")]):
-                for refseq in tx.get("refseq_identifiers"):
-                    refseq_version = fetch_refseq_version(refseq)  # adds version to a refseq ID
-                    hgvs_simple = ":".join([refseq_version, tx["coding_sequence_name"]])
+            mane_plus_clinical = tx.get("mane_plus_clinical_transcript")
+
+            for refseq in tx.get("refseq_identifiers", []):
+                refseq_version = fetch_refseq_version(refseq)  # Adds version to a RefSeq ID
+                hgvs_simple = f"{refseq_version}:{coding_seq_name}"
+
+                refseq_is_mane_select = mane_select == refseq_version
+                refseq_is_mane_plus_clinical = mane_plus_clinical == refseq_version
 
-                    # Validate descriptor using VariantValidator
-                    validated = validate_hgvs(build, hgvs_simple)
+                # Transcript is validate only when conditions are met
+                validated = (
+                    validate_hgvs(build, hgvs_simple)
+                    if (case_has_build_37 or refseq_is_mane_select or refseq_is_mane_plus_clinical)
+                    else ""
+                )
 
-                    label = hgvs_simple
-                    if validated:
-                        label += "_validated_"
+                label = f"{hgvs_simple}{'_validated_' if validated else ''}{'_mane-select_' if refseq_is_mane_select else ''}{'_mane-plus-clinical_' if refseq_is_mane_plus_clinical else ''}"
 
-                    if mane_select and mane_select == refseq_version:
-                        label += "_mane-select_"
+                tx_hgvs_list.append((hgvs_simple, label))
 
-                    tx_hgvs_list.append((hgvs_simple, label))
     return tx_hgvs_list
 
 
@@ -604,8 +619,12 @@ def remove_item_from_submission(submission: str, object_type: str, subm_variant_
     if object_type == "variant_data":
         variant_id: str = subm_variant_id.split("_")[-1]
         variant_obj: dict = store.variant(document_id=variant_id)
+        if not variant_obj:
+            return
+        case_obj = store.case(case_id=variant_obj["case_id"])
+        if not case_obj:
+            return
         institute_obj: dict = store.institute(institute_id=variant_obj["institute"])
-        case_obj: dict = store.case(case_id=variant_obj["case_id"])
         user_obj: dict = store.user(user_id=current_user._id)
         for category in ["case", "variant"]:
             store.create_event(

scout/server/blueprints/clinvar/templates/clinvar/clinvar_submissions.html

@@ -126,13 +126,19 @@
             </thead>
             <tbody>
               {% set var_key_name = {} %}
+
               {% for subm_variant in subm_obj.variant_data  %} <!-- loop over the submitted variants-->
+                {% set case_name = subm_obj.cases[subm_variant.case_id] %}
                 <tr>
                   <td>{{loop.index}}</td>
                     {% if subm_variant.category == 'sv' %}
                       {% do var_key_name.update( {subm_variant.local_id : '_'.join([subm_variant.var_type, subm_variant.chromosome, subm_variant.breakpoint1 or subm_variant.outer_start or ""]) }) %}
                       <td>
-                        <a href="{{ url_for('variant.sv_variant', institute_id=institute._id, case_name=subm_obj.cases[subm_variant.case_id], variant_id=subm_variant.local_id) }}" target="_blank" rel="noopener"><strong>{{var_key_name[subm_variant.local_id]|truncate(25,true,'..')}}</strong></a>
+                        {% if "N/A" not in case_name %}
+                          <a href="{{ url_for('variant.sv_variant', institute_id=institute._id, case_name=case_name, variant_id=subm_variant.local_id) }}" target="_blank" rel="noopener"><strong>{{var_key_name[subm_variant.local_id]|truncate(25,true,'..')}}</strong></a>
+                        {% else %}
+                          {{ var_key_name[subm_variant.local_id]|truncate(25,true,'..') }} (N/A)
+                        {% endif %}
                       </td>
                       <td><button id="{{subm_variant._id}}" type="button" class="btn btn-primary btn-xs var_btn"><span class="fa fa-search-plus" aria-hidden="true"></span></button></td>
                       <td><div class="badge bg-warning">SV</div></td>
@@ -143,21 +149,27 @@
                         {% do var_key_name.update({subm_variant.local_id : '_'.join([subm_variant.chromosome, subm_variant.start, subm_variant.ref[0:5], subm_variant.alt[0:5]]) }) %}
                       {% endif %}
                       <td>
-                        <a href="{{ url_for('variant.variant', institute_id=institute._id, case_name=subm_obj.cases[subm_variant.case_id], variant_id=subm_variant.local_id) }}" target="_blank" rel="noopener"><strong>{{var_key_name[subm_variant.local_id]|truncate(25,true,'..')}}</strong></a>
+                        {% if "N/A" not in case_name %}
+                          <a href="{{ url_for('variant.variant', institute_id=institute._id, case_name=case_name, variant_id=subm_variant.local_id) }}" target="_blank" rel="noopener"><strong>{{var_key_name[subm_variant.local_id]|truncate(25,true,'..')}}</strong></a>
+                        {% else %}
+                          {{ var_key_name[subm_variant.local_id]|truncate(25,true,'..') }} (N/A)
+                        {% endif %}
                       </td>
                       <td><button id="{{subm_variant._id}}" type="button" class="btn btn-primary btn-xs var_btn"><span class="fa fa-search-plus" aria-hidden="true"></span></button></td>
                       <td><div class="badge bg-success">SNV</div></td>
                     {% endif %}
                   </td>
-                  <td><a href="{{ url_for('cases.case', institute_id=institute._id, case_name=subm_obj.cases[subm_variant.case_id]) }}" target="_blank" rel="noopener">{{subm_obj.cases[subm_variant.case_id]}}</a></td>
+                  <td>{{ case_link(institute_id=institute._id, case_name=case_name) }}</td>
                   <td>{{subm_variant.ref_seq or '-'}}</td>
                   <td>{{subm_variant.gene_symbol or '-'}}</td>
                   <td>{{subm_variant.hgvs|truncate(100,true,'..') or '-'}}</td>
                   <td>{{subm_variant.clinsig}}</td>
                   <td>{{subm_variant.added_by or "N/A"}}</td>
-                  <form id="delete_variant_{{subm_variant._id}}" action="{{ url_for('clinvar.clinvar_delete_object', submission=subm_obj._id, object_type='variant_data') }}" method="POST">
-                    <td><button type="submit" name="delete_object" value="{{subm_variant._id}}" class="btn btn-danger btn-xs"><span class="fa fa-trash" aria-hidden="true"></span></button></td>
-                  </form>
+                  <td>
+                    <form id="delete_variant_{{subm_variant._id}}" action="{{ url_for('clinvar.clinvar_delete_object', submission=subm_obj._id, object_type='variant_data') }}" method="POST">
+                      <button type="submit" name="delete_object" value="{{subm_variant._id}}" class="btn btn-danger btn-xs"><span class="fa fa-trash" aria-hidden="true"></span></button>
+                    </form>
+                  </td>
                 </tr>
                 <tr>
                   <td colspan=11>
@@ -191,9 +203,9 @@
               <thead>
                 <tr>
                   <th></th>
-                  <th>Individual ID</th>
+                  <th>Individual</th>
                   <th></th>
-                  <th>Case ID</th>
+                  <th>Case</th>
                   <th>Variant</th>
                   <th>Allele origin</th>
                   <th></th>
@@ -209,12 +221,14 @@
                     </td>
                     </form>
                     <td><button id="{{case._id}}" type="button" class="btn btn-primary btn-xs cd_btn"><span class="fa fa-search-plus" aria-hidden="true"></span></button></td>
-                    <td><a href="{{ url_for('cases.case', institute_id=institute._id, case_name=subm_obj.cases[case.case_id]) }}" target="_blank" rel="noopener">{{subm_obj.cases[case.case_id]}}</a></td>
+                    <td>{{ case_link(institute_id=institute._id, case_name=subm_obj.cases[case.case_id]) }}</td>
                     <td>{{var_key_name[case.linking_id]|truncate(100,true,'..')}}</td>
                     <td>{{case.allele_origin}}</td>
-                    <form id="delete_casedata_{{case._id}}" action="{{ url_for('clinvar.clinvar_delete_object', submission=subm_obj._id, object_type='case_data') }}" method="POST">
-                      <td><button type="submit" name="delete_object" value="{{case._id}}" class="btn btn-danger btn-xs"><span class="fa fa-trash" aria-hidden="true"></span></button></td>
-                    </form>
+                    <td>
+                      <form id="delete_casedata_{{case._id}}" action="{{ url_for('clinvar.clinvar_delete_object', submission=subm_obj._id, object_type='case_data') }}" method="POST">
+                        <button type="submit" name="delete_object" value="{{case._id}}" class="btn btn-danger btn-xs"><span class="fa fa-trash" aria-hidden="true"></span></button>
+                      </form>
+                    </td>
                   </tr>
                   <tr>
                     <td colspan=8>
@@ -242,6 +256,14 @@
 </div>
 {% endmacro %}
 
+{% macro case_link(institute_id, case_name) %}
+{% if "N/A" in case_name %}
+  {{ case_name }}
+{% else %}
+  <a href="{{ url_for('cases.case', institute_id=institute_id, case_name=case_name) }}" target="_blank">{{case_name}}</a>
+{% endif %}
+{% endmacro %}
+
 {% macro action_modal(action_type, subm_id) %}
 <div class="modal fade" id="{{action_type}}Modal_{{subm_id}}" tabindex="-1">
   <div class="modal-dialog">

scout/server/blueprints/clinvar/templates/clinvar/multistep_add_variant.html

@@ -81,7 +81,7 @@
                   </div>
                   <div class="my-2 mx-lg-2" style="width:30%; display: inline">{{variant_data.var_form.assertion_method_cit_id(class="bg-white")}}</div>
                   </div>
-
+                <input type="button" name="previous" class="previous action-button-previous" value="Previous"/>
                 <input type="button" name="next" class="next action-button" value="Next"/>
               </fieldset>
               <fieldset data-step="3">
@@ -92,7 +92,7 @@
                   {% if var_category == 'snv' %}
                     <br><br>
                     <!-- Transcripts & HGVS:(optional) -->
-                    {{variant_data.var_form.tx_hgvs.label(class="fw-bold, text-dark")}}
+                    {{ variant_data.var_form.tx_hgvs.label(class="fw-bold, text-dark") }}
 
                     <span class="text-danger" data-bs-toggle='tooltip' title="If you do not provide any HGVS expression, chromosome coordinates will be used to describe this variant instead (automatic). HGVS expressions were validated using VariantValidator"><strong>?</strong></span>
                     <span class="badge bg-primary float-end"><a class="text-white" href="https://variantvalidator.org/service/validate/" target="_blank" rel="noopener">VariantValidator</a></span>
@@ -101,7 +101,7 @@
                     {% with messages = get_flashed_messages() %}
                       {% if messages %}
                         {% for message in messages %}
-                          <span class="ml-3" style="color:red">{{ message }}</span><br>
+                          <span class="ml-3">{{ message }}</span><br>
                         {% endfor %}
                         <br><br>
                       {% endif %}
@@ -113,14 +113,17 @@
                     {% for item_row in variant_data.var_form.tx_hgvs | batch(3) %}
                       <tr>
                       {% for item in item_row %}
-                        {% set ns = namespace(label='', validated=false, mane_select=false) %}
-
+                        {% set ns = namespace(label='', validated=false, mane_select=false, mane_plus_clinical=false) %}
                         {% if "_validated_" in item.label.text %}
                           {% set ns.validated = true %}
                         {% endif %}
                         {% if "_mane-select_" in item.label.text %}
                           {% set ns.mane_select = true %}
                         {% endif %}
+                        {% if "_mane-plus-clinical_" in item.label.text %}
+                           {% set ns.mane_plus_clinical = true %}
+                        {% endif %}
+
                         {% set ns.label = item.label.text | replace("_validated_", "") | replace("_mane-select_", "")  %}
 
                         <td style="width: 3%; text-align: right; vertical-align: baseline;">
@@ -138,6 +141,9 @@
                           {% if ns.mane_select %}
                             <span class='badge bg-dark'>MANE SELECT</span>
                           {% endif %}
+                          {% if ns.mane_plus_clinical %}
+                            <span class='badge bg-dark'>MANE PLUS CLINICAL</span>
+                          {% endif %}
                           {% if ns.validated %}
                             <em class="fa fa-check text-success" aria-hidden="true" data-bs-toggle="tooltip" title="Verified by VariantValidator"></em>
                           {% endif %}
@@ -147,6 +153,9 @@
                       </tr>
                     {% endfor %}
                     </table>
+
+                    <span class="text-danger">HGVS validation is performed only for variants in build GRCh37 or MANE Select and MANE Plus Clinical transcripts. For any other available HGVS present in this list, manual validation can be performed using the VariantValidator link above.</span>
+
                     <br><br>
                     <!-- dbSNP identifier -->
                     {{variant_data.var_form.variations_ids.label(class="fw-bold, text-dark")}}

scout/server/blueprints/clinvar/views.py

@@ -3,10 +3,22 @@ from json import dumps
 from tempfile import NamedTemporaryFile
 from typing import List, Tuple
 
-from flask import Blueprint, flash, redirect, render_template, request, send_file, url_for
+from flask import (
+    Blueprint,
+    flash,
+    redirect,
+    render_template,
+    request,
+    send_file,
+    url_for,
+)
 from flask_login import current_user
 
-from scout.constants.clinvar import CASEDATA_HEADER, CLINVAR_HEADER, GERMLINE_CLASSIF_TERMS
+from scout.constants.clinvar import (
+    CASEDATA_HEADER,
+    CLINVAR_HEADER,
+    GERMLINE_CLASSIF_TERMS,
+)
 from scout.server.extensions import clinvar_api, store
 from scout.server.utils import institute_and_case
 

scout/server/blueprints/diagnoses/static/diagnoses.js

@@ -135,7 +135,14 @@ function initialiseTable(data) {
     $('#diagnoses_table').DataTable({
         data: data,
         paging: true,
-        dom: 'Brtip',
+        layout: {
+					topStart: 'buttons',
+					topEnd: {
+							search: {
+									placeholder: 'Filter further...'
+							}
+					}
+				},
         buttons: [
             {
                 extend: 'excelHtml5',

scout/server/blueprints/institutes/controllers.py

@@ -391,8 +391,16 @@ def update_institute_settings(store: MongoAdapter, institute_obj: Dict, form: Mu
     updated_institute = store.update_institute(
         internal_id=institute_obj["_id"],
         sanger_recipients=get_sanger_recipients(form),
-        coverage_cutoff=int(form.get("coverage_cutoff")),
-        frequency_cutoff=float(form.get("frequency_cutoff")),
+        coverage_cutoff=(
+            int(form["coverage_cutoff"])
+            if form.get("coverage_cutoff")
+            else form.get("coverage_cutoff")
+        ),
+        frequency_cutoff=(
+            float(form["frequency_cutoff"])
+            if form.get("frequency_cutoff")
+            else form.get("frequency_cutoff")
+        ),
         show_all_cases_status=form.getlist("show_all_cases_status"),
         display_name=form.get("display_name"),
         phenotype_groups=phenotype_groups,

scout/server/blueprints/institutes/static/variants_list_scripts.js

@@ -1,7 +1,15 @@
 $(document).ready(function() {
   $('#variants_table').DataTable( {
       paging: false,
-      dom: 'Bfrtip',
+			searching: true,
+			layout: {
+				topStart: 'buttons',
+				topEnd: {
+            search: {
+                placeholder: 'Search'
+            }
+        }
+			},
       buttons: [
           'copyHtml5',
           'excelHtml5',

scout/server/blueprints/institutes/templates/overview/institute_sidebar.html

@@ -51,7 +51,15 @@
           </div>
       </a>
 
-    <!-- Variant filters -->
+     <!-- MME data menu item -->
+      <a href="{{ url_for('mme.mme_submissions', institute_id=institute._id) }}" class="bg-dark list-group-item list-group-item-action flex-column align-items-start">
+          <div class="d-flex w-100 justify-content-start align-items-center">
+              <span class="fas fa-people-arrows me-3"></span>
+              <span class="menu-collapsed">MME submissions</span>
+          </div>
+      </a>
+
+     <!-- Variant filters -->
       <a href="{{ url_for('overview.filters', institute_id=institute._id) }}" class="bg-dark list-group-item list-group-item-action flex-column align-items-start">
           <div class="d-flex w-100 justify-content-start align-items-center">
               <span class="fa fa-filter me-3"></span>