#1157 - Variant details - few minor things, eg AlphaMissense help, sh…

…ow gnomAD version

snpdb/migrations/0144_add_vgc_descriptions.py

@@ -0,0 +1,27 @@
+# Generated by Django 4.2.15 on 2024-09-09 06:24
+
+from django.db import migrations
+
+
+def _add_vgc_descriptions(apps, _schema_editor):
+    VariantGridColumn = apps.get_model("snpdb", "VariantGridColumn")
+
+    VGC_DESCRIPTIONS = {
+        "alphamissense_rankscore": "AlphaMissense is an AI model developed by DeepMind that predicts pathogenicity of missense variants. See <a href='https://www.science.org/doi/10.1126/science.adg7492'>Paper</a>",
+        "mavedb_urn": "DB identifier from <a href='https://www.mavedb.org/'>MaveDB</a> - a public repository for datasets from Multiplexed Assays of Variant Effect (MAVEs), such as those generated by deep mutational scanning or massively parallel reporter assay experiments.",
+        "mavedb_score": "Score from <a href='https://www.mavedb.org/'>MaveDB</a> - a public repository for datasets from Multiplexed Assays of Variant Effect (MAVEs), such as those generated by deep mutational scanning or massively parallel reporter assay experiments.",
+    }
+
+    for pk, description in VGC_DESCRIPTIONS.items():
+        VariantGridColumn.objects.filter(pk=pk).update(description=description)
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('snpdb', '0143_one_off_rename_clinvar_variantgridcolumns'),
+    ]
+
+    operations = [
+        migrations.RunPython(_add_vgc_descriptions, reverse_code=migrations.RunPython.noop)
+    ]

variantopedia/templates/variantopedia/variant_details.html

@@ -70,6 +70,7 @@
     "grantham": [57, 105],
     "gerp_pp_rs": [0, 3],
     //
+    "alphamissense_rankscore": pathogenicity_rankscore_threshold,
     "cadd_raw_rankscore": pathogenicity_rankscore_threshold,
     "revel_rankscore": pathogenicity_rankscore_threshold,
     "bayesdel_noaf_rankscore": pathogenicity_rankscore_threshold,
@@ -427,6 +428,7 @@
 function applyVariantValues() {
     // Render variant annotation values this way so it's colored correctly etc as it
     // goes through the same formatting as transcript JavaScript values if done through here
+    applyValue("alphamissense_rankscore", {{ variant_annotation.bayesdel_noaf_rankscore | jsonify}});
     applyValue("bayesdel_noaf_rankscore", {{ variant_annotation.bayesdel_noaf_rankscore | jsonify}});
     applyValue("cadd_raw_rankscore", {{ variant_annotation.cadd_raw_rankscore | jsonify}});
     applyValue("clinpred_rankscore", {{ variant_annotation.clinpred_rankscore | jsonify}});
@@ -730,6 +732,7 @@ <h4>Tags</h4>
                         {% labelled id='af_uk10k' label='UK10K' help=annotation_description.af_uk10k hint="tiny" value_css="text-monospace" %}{{ variant_annotation.af_uk10k|format_unit_as_percent }}{% endlabelled %}
                         {% labelled id='topmed_af' label='TopMed' help=annotation_description.topmed_af hint="tiny" value_css="text-monospace" %}{{ variant_annotation.topmed_af|format_unit_as_percent }}{% endlabelled %}
                     {% endif %}
+                        {% labelled label='gnomAD version' hint='tiny' %}{{ variant_annotation.version.gnomad }}{% endlabelled %}
                         {% if variant_annotation.gnomad_af %}
                             {% labelled id='gnomad_af' label='gnomAD Allele Frequency' help=annotation_description.gnomad_af hint="tiny" value_css="text-monospace" %}{{ variant_annotation.gnomad_af|format_unit_as_percent }}{% endlabelled %}
                             {% if variant_annotation.has_gnomad_faf %}
@@ -747,7 +750,7 @@ <h4>Tags</h4>
                                 {% labelled label="gnomAD Is Filtered" help=annotation_description.gnomad_filtered hint="tiny" %}{% endlabelled %}
                             {% endif %}
 
-                            {% labelled id='gnomad_total_homozygotes' label='gnomAD Total Homozygotes' help=annotation_description.gnomad_total_homozygotes hint="tiny" value_css="text-monospace" %}{{ variant_annotation.gnomad_hom_alt }}{% endlabelled %}
+                            {% labelled id='gnomad_total_homozygotes' label='gnomAD Total Homozygotes' help=annotation_description.gnomad_hom_alt hint="tiny" value_css="text-monospace" %}{{ variant_annotation.gnomad_hom_alt }}{% endlabelled %}
                             {% if variant_annotation.has_extended_gnomad_fields %}
                                 {% labelled id='gnomad_ac' label='gnomAD Alt Allele Count' help=annotation_description.gnomad_ac hint="tiny" value_css="text-monospace" %}{{ variant_annotation.gnomad_ac }}{% endlabelled %}
                                 {% labelled id='gnomad_an' label='gnomAD Total number of alleles' help=annotation_description.gnomad_an hint="tiny" value_css="text-monospace" %}{{ variant_annotation.gnomad_an }}{% endlabelled %}
@@ -808,7 +811,7 @@ <h4>Tags</h4>
                                 {% labelled id='gnomad_sas_af' label='South Asian' help=annotation_description.gnomad_sas_af hint="tiny" value_css="text-monospace" %}{{ variant_annotation.gnomad_sas_af|format_unit_as_percent }}{% endlabelled %}
                             </div>
                         {% else %}
-                            {% labelled id='gnomad_none' label='gnomAD' hint="tiny" %}No gnomAD entry{% endlabelled %}
+                            {% labelled id='gnomad_none' label='gnomAD' hint="tiny" help=annotation_description.gnomad %}No gnomAD entry{% endlabelled %}
                         {% endif %}
                     </div>
                 </div>
@@ -826,7 +829,7 @@ <h4>Tags</h4>
                             <span id="maxentscan_alt"></span>&nbsp;<span class="text-secondary">Alt</span>,
                             <span id="maxentscan_diff"></span>&nbsp;<span class="text-secondary">Diff</span>
                         {% endlabelled %}
-                        {% labelled label="MexEnt %Diff/Ref" hint="tiny" %}<span id="maxentscan_percent_diff_ref" data-suffix="%"></span>{% endlabelled %}
+                        {% labelled label="MaxEnt %Diff/Ref" help=annotation_description.maxentscan_percent_diff_ref hint="tiny" %}<span id="maxentscan_percent_diff_ref" data-suffix="%"></span>{% endlabelled %}
                         {% labelled id="dbscsnv_ada_score" label="dbscSNV (Ada)" help=annotation_description.dbscsnv_ada_score hint="tiny" %}{{ variant_annotation.dbscsnv_ada_score|floatformat:2 }}{% endlabelled %}
                         {% labelled id="dbscsnv_rf_score" label="dbscSNV (RF)" help=annotation_description.dbscsnv_rf_score hint="tiny" %}{{ variant_annotation.dbscsnv_rf_score|floatformat:2 }}{% endlabelled %}
 
@@ -875,7 +878,7 @@ <h4>Tags</h4>
                         {% labelled id='dbsnp_rs_id' label='dbSNP' help=annotation_description.dbsnp_rs_id hint="tiny" %}{{ variant_annotation.dbsnp_rs_id }}{% endlabelled %}
                         {% labelled id='ensembl_protein' label='Ensembl Protein' help=annotation_description.ensembl_protein hint="tiny" %}{% endlabelled %}
                     {% if variant_annotation.has_mavedb %}
-                        {% labelled id='mave_db_url' label='MaveDB' help=annotation_description.mave_db_url hint='tiny' %}
+                        {% labelled id='mave_db_url' label='MaveDB' help=annotation_description.mave_db hint='tiny' %}
                             {% with mave_urls=variant_annotation.get_mave_urls %}
                                 {% for label, url in mave_urls.items %}
                                     <a target="_blank" class='hover-link' href="{{ url }}">{{ label }}</a>
@@ -925,7 +928,7 @@ <h4>Tags</h4>
                                 {% endfor %}
                             {% endlabelled %}
                         {% else %}
-                            {% labelled label="Mastermind" hint="tiny" %}No local Mastermind entry<br><i>may be others on site</i>{% endlabelled %}
+                            {% labelled label="Mastermind" hint="tiny" help=annotation_description.mastermind %}No local Mastermind entry<br><i>may be others on site</i>{% endlabelled %}
                         {% endif %}
 
                     </div>

variantopedia/views.py

@@ -593,6 +593,9 @@ def variant_details_annotation_version(request, variant_id, annotation_version_i
         annotation_description = VariantGridColumn.get_column_descriptions()
         annotation_description["allele"] = "An Allele is genome build independent - ie GRCh37 and GRCh38 variants for" \
                                            " the same change are linked by an allele"
+        annotation_description["gnomad"] = "<a href='https://gnomad.broadinstitute.org/'>gnomAD</a> is the world's largest population frequency database"
+        annotation_description["mastermind"] = "Mastermind indexes medical literature for variants and genes, see <a href='https://www.genomenon.com/data'>Mastermind</a>"  # Used for no results
+        annotation_description["mave_db"] = "<a href='https://www.mavedb.org/'>MaveDB</a> is a public repository for datasets from Multiplexed Assays of Variant Effect (MAVEs), such as those generated by deep mutational scanning or massively parallel reporter assay experiments."
         annotation_description["maxentscan"] = "<a href='http://hollywood.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html'>MaxEntScan</a> scores for human 5 prime splice sites."
         annotation_description["spliceai"] = "Deep Learning splicing predictor - see <a href='https://www.sciencedirect.com/science/article/pii/S0092867418316295?via%3Dihub'>SpliceAI</a>"