diff --git a/snpdb/migrations/0144_add_vgc_descriptions.py b/snpdb/migrations/0144_add_vgc_descriptions.py
new file mode 100644
index 000000000..0af72c702
--- /dev/null
+++ b/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 Paper",
+ "mavedb_urn": "DB identifier from MaveDB - 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 MaveDB - 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)
+ ]
diff --git a/variantopedia/templates/variantopedia/variant_details.html b/variantopedia/templates/variantopedia/variant_details.html
index 17043e5dc..08aee4bc0 100644
--- a/variantopedia/templates/variantopedia/variant_details.html
+++ b/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 @@ Tags
{% 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 @@ Tags
{% 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 @@ Tags
{% 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 %}
{% 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 %}
@@ -826,7 +829,7 @@ Tags
Alt,
Diff
{% endlabelled %}
- {% labelled label="MexEnt %Diff/Ref" hint="tiny" %}{% endlabelled %}
+ {% labelled label="MaxEnt %Diff/Ref" help=annotation_description.maxentscan_percent_diff_ref hint="tiny" %}{% 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 @@ Tags
{% 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 %}
{{ label }}
@@ -925,7 +928,7 @@ Tags
{% endfor %}
{% endlabelled %}
{% else %}
- {% labelled label="Mastermind" hint="tiny" %}No local Mastermind entry
may be others on site{% endlabelled %}
+ {% labelled label="Mastermind" hint="tiny" help=annotation_description.mastermind %}No local Mastermind entry
may be others on site{% endlabelled %}
{% endif %}
diff --git a/variantopedia/views.py b/variantopedia/views.py
index 57a2f7d38..93bb6a110 100644
--- a/variantopedia/views.py
+++ b/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"] = "gnomAD is the world's largest population frequency database"
+ annotation_description["mastermind"] = "Mastermind indexes medical literature for variants and genes, see Mastermind" # Used for no results
+ annotation_description["mave_db"] = "MaveDB 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"] = "MaxEntScan scores for human 5 prime splice sites."
annotation_description["spliceai"] = "Deep Learning splicing predictor - see SpliceAI"