diff --git a/scout/adapter/mongo/query.py b/scout/adapter/mongo/query.py
index 3ec4fe991..914733acc 100644
--- a/scout/adapter/mongo/query.py
+++ b/scout/adapter/mongo/query.py
@@ -12,6 +12,7 @@ class QueryHandler(object):
                 'genetic_models': list,
                 'thousand_genomes_frequency': float,
                 'exac_frequency': float,
+                'clingen_ngi': int,
                 'cadd_score': float,
                 'cadd_inclusive": boolean,
                 'genetic_models': list(str),
@@ -24,6 +25,7 @@ class QueryHandler(object):
                 'chrom': str,
                 'start': int,
                 'end': int,
+                'svtype': list,
                 'gene_panels': list(str),
             }
 
@@ -144,6 +146,14 @@ class QueryHandler(object):
                 ]
             })
 
+        if query.get('clingen_ngi') is not None:
+            mongo_query_minor.append({
+                '$or': [
+                    {'clingen_ngi': {'$exists': False}},
+                    {'clingen_ngi': {'$lt': query['clingen_ngi'] + 1}},
+                ]
+            })
+
         if query.get('cadd_score') is not None:
             cadd = query['cadd_score']
             cadd_query = {'cadd_score': {'$gt': float(cadd)}}
diff --git a/scout/server/blueprints/variants/forms.py b/scout/server/blueprints/variants/forms.py
index bab4716d7..407cbe9d7 100644
--- a/scout/server/blueprints/variants/forms.py
+++ b/scout/server/blueprints/variants/forms.py
@@ -90,3 +90,4 @@ class SvFiltersForm(FlaskForm):
     svtype = SelectMultipleField('SVType', choices=SV_TYPE_CHOICES)
 
     thousand_genomes_frequency = BetterDecimalField('1000 Genomes', places=2)
+    clingen_ngi = IntegerField('ClinGen NGI obs')
diff --git a/scout/server/blueprints/variants/templates/variants/sv-variant.html b/scout/server/blueprints/variants/templates/variants/sv-variant.html
index e4e54740a..249c9cb4b 100644
--- a/scout/server/blueprints/variants/templates/variants/sv-variant.html
+++ b/scout/server/blueprints/variants/templates/variants/sv-variant.html
@@ -93,8 +93,11 @@
           Position
           <div class="pull-right">
             <a class="md-label" href="{{ url_for('pileup.viewer', bam=case.bam_files, bai=case.bai_files, sample=case.sample_names, contig=variant.chromosome, start=(variant.position - 50), stop=(variant.end + 50), vcf=case.vcf_files.vcf_sv) }}" target="_blank">
-              Alignment: {{ variant.chromosome }}:{{ variant.position }}-{{ variant.end }}
-            </a>
+              Alignment: {{ variant.chromosome }}
+            </a>:
+            <a class="md-label" href="{{ url_for('pileup.viewer', bam=case.bam_files, bai=case.bai_files, sample=case.sample_names, contig=variant.chromosome, start=(variant.position - 500), stop=(variant.position + 500), vcf=case.vcf_files.vcf_sv) }}" target="_blank">
+{{ variant.position }}</a> -
+            <a class="md-label" href="{{ url_for('pileup.viewer', bam=case.bam_files, bai=case.bai_files, sample=case.sample_names, contig=variant.chromosome, start=(variant.end - 500), stop=(variant.end + 500), vcf=case.vcf_files.vcf_sv) }}" target="_blank">{{ variant.end }}</a>
           </div>
         </li>
 	      <li class="list-group-item">
diff --git a/scout/server/blueprints/variants/templates/variants/sv-variants.html b/scout/server/blueprints/variants/templates/variants/sv-variants.html
index 4a20b3618..5c4674b10 100644
--- a/scout/server/blueprints/variants/templates/variants/sv-variants.html
+++ b/scout/server/blueprints/variants/templates/variants/sv-variants.html
@@ -152,6 +152,8 @@
           {{ form.thousand_genomes_frequency(class="form-control") }}
         </div>
         <div class="col-xs-3">
+	  {{ form.clingen_ngi.label(class="control-label") }}
+	  {{ form.clingen_ngi(class="form-control") }}
         </div>
         <div class="col-xs-3">
           {{ form.svtype.label(class="control-label") }}
@@ -177,6 +179,7 @@
                           functional_annotations=severe_so_terms,
                           region_annotations=['exonic', 'splicing'],
                           thousand_genomes_frequency=institute.frequency_cutoff,
+			  clingen_ngi=15,
 			  size=100,
                           gene_panels=form.data.get('gene_panels')) }}"
                  class="btn btn-default form-control">
@@ -258,7 +261,11 @@
         <div>{{ annotation }}</div>
       {% endfor %}
     </td>
-    <td>{{ variant.thousand_genomes_frequency|human_decimal if variant.thousand_genomes_frequency }}</td>
+    <td>
+      {% if variant.thousand_genomes_frequency %}
+        {{ variant.thousand_genomes_frequency|human_decimal }}
+      {% endif %}
+    </td>
     <td>
       <div class="flex">
         <div>

SV frequency filter
- [x] add filter boxes for filter frequencies of interest (e.g. ClinGen NGI, array, SweGen)
- [x] clinical filter settings update for structural variants
- [x] clickable coordinates for start end of structural variant to enable view the edges of large variants

diff --git a/tests/adapter/test_query.py b/tests/adapter/test_query.py
index d6c424276..bad5131af 100644
--- a/tests/adapter/test_query.py
+++ b/tests/adapter/test_query.py
@@ -195,6 +195,22 @@ def test_build_chrom(adapter):
 
     assert mongo_query['chromosome'] == chrom
 
+
+def test_build_ngi_sv(adapter):
+    case_id = 'cust000'
+    count = 1
+    query = {'clingen_ngi': count}
+    
+    mongo_query = adapter.build_query(case_id, query=query)
+    assert  mongo_query['$and'] == [
+        {
+            '$or':[
+                {'clingen_ngi': {'$exists': False}},
+                {'clingen_ngi': {'$lt': query['clingen_ngi'] + 1}}
+            ]
+        }
+    ]
+
 def test_build_range(adapter):
     case_id = 'cust000'
     chrom = '1'

pip install -e .
parse_log_pytest
requirements.txt
pytest
3.9
requirements.txt
pytest --no-header -rA --tb=line --color=no -p no:cacheprovider -W ignore::DeprecationWarning
babel==2.17.0
blinker==1.9.0
cachelib==0.13.0
certifi==2025.1.31
charset-normalizer==3.4.1
click==8.1.8
coloredlogs==15.0.1
Cython==3.0.12
cyvcf2==0.31.1
dnspython==2.7.0
dominate==2.9.1
exceptiongroup==1.2.2
Flask==3.1.0
flask-babel==4.0.0
Flask-Bootstrap==3.3.7.1
Flask-DebugToolbar==0.16.0
Flask-Login==0.6.3
Flask-Mail==0.10.0
Flask-Markdown==0.3
Flask-OAuthlib==0.9.6
Flask-PyMongo==3.0.1
Flask-WTF==1.2.2
humanfriendly==10.0
idna==3.10
importlib_metadata==8.6.1
iniconfig==2.1.0
intervaltree==3.1.0
itsdangerous==2.2.0
Jinja2==3.1.6
livereload==2.7.1
loqusdb==2.6.0
Markdown==3.7
MarkupSafe==3.0.2
mongo-adapter==0.3.3
mongomock==4.3.0
numpy==2.0.2
oauthlib==2.1.0
packaging==24.2
path==17.1.0
path.py==12.5.0
ped-parser==1.6.6
pluggy==1.5.0
pymongo==4.11.3
pytest==8.3.5
python-dateutil==2.9.0.post0
pytz==2025.2
PyYAML==6.0.2
query-phenomizer==1.2.1
requests==2.32.3
requests-oauthlib==1.1.0
-e git+https://github.com/Clinical-Genomics/scout.git@96e4730530858967fd3b1542c79cc5a7f77ece12#egg=scout_browser
sentinels==1.0.0
six==1.17.0
sortedcontainers==2.4.0
tomli==2.2.1
tornado==6.4.2
urllib3==2.3.0
vcftoolbox==1.5.1
visitor==0.1.3
Werkzeug==3.1.3
WTForms==3.2.1
zipp==3.21.0

name: scout
channels:
  - defaults
  - https://repo.anaconda.com/pkgs/main
  - https://repo.anaconda.com/pkgs/r
  - conda-forge
dependencies:
  - _libgcc_mutex=0.1=main
  - _openmp_mutex=5.1=1_gnu
  - ca-certificates=2025.2.25=h06a4308_0
  - ld_impl_linux-64=2.40=h12ee557_0
  - libffi=3.4.4=h6a678d5_1
  - libgcc-ng=11.2.0=h1234567_1
  - libgomp=11.2.0=h1234567_1
  - libstdcxx-ng=11.2.0=h1234567_1
  - ncurses=6.4=h6a678d5_0
  - openssl=3.0.16=h5eee18b_0
  - pip=25.0=py39h06a4308_0
  - python=3.9.21=he870216_1
  - readline=8.2=h5eee18b_0
  - setuptools=75.8.0=py39h06a4308_0
  - sqlite=3.45.3=h5eee18b_0
  - tk=8.6.14=h39e8969_0
  - tzdata=2025a=h04d1e81_0
  - wheel=0.45.1=py39h06a4308_0
  - xz=5.6.4=h5eee18b_1
  - zlib=1.2.13=h5eee18b_1
  - pip:
      - babel==2.17.0
      - blinker==1.9.0
      - cachelib==0.13.0
      - certifi==2025.1.31
      - charset-normalizer==3.4.1
      - click==8.1.8
      - coloredlogs==15.0.1
      - cython==3.0.12
      - cyvcf2==0.31.1
      - dnspython==2.7.0
      - dominate==2.9.1
      - exceptiongroup==1.2.2
      - flask==3.1.0
      - flask-babel==4.0.0
      - flask-bootstrap==3.3.7.1
      - flask-debugtoolbar==0.16.0
      - flask-login==0.6.3
      - flask-mail==0.10.0
      - flask-markdown==0.3
      - flask-oauthlib==0.9.6
      - flask-pymongo==3.0.1
      - flask-wtf==1.2.2
      - humanfriendly==10.0
      - idna==3.10
      - importlib-metadata==8.6.1
      - iniconfig==2.1.0
      - intervaltree==3.1.0
      - itsdangerous==2.2.0
      - jinja2==3.1.6
      - livereload==2.7.1
      - loqusdb==2.6.0
      - markdown==3.7
      - markupsafe==3.0.2
      - mongo-adapter==0.3.3
      - mongomock==4.3.0
      - numpy==2.0.2
      - oauthlib==2.1.0
      - packaging==24.2
      - path==17.1.0
      - path-py==12.5.0
      - ped-parser==1.6.6
      - pluggy==1.5.0
      - pymongo==4.11.3
      - pytest==8.3.5
      - python-dateutil==2.9.0.post0
      - pytz==2025.2
      - pyyaml==6.0.2
      - query-phenomizer==1.2.1
      - requests==2.32.3
      - requests-oauthlib==1.1.0
      - sentinels==1.0.0
      - six==1.17.0
      - sortedcontainers==2.4.0
      - tomli==2.2.1
      - tornado==6.4.2
      - urllib3==2.3.0
      - vcftoolbox==1.5.1
      - visitor==0.1.3
      - werkzeug==3.1.3
      - wtforms==3.2.1
      - zipp==3.21.0
prefix: /opt/conda/envs/scout

tests/adapter/test_query.py::test_build_ngi_sv
tests/adapter/test_query.py::test_build_query tests/adapter/test_query.py::test_build_thousand_g_query tests/adapter/test_query.py::test_build_non_existing_thousand_g tests/adapter/test_query.py::test_build_cadd_exclusive tests/adapter/test_query.py::test_build_cadd_inclusive tests/adapter/test_query.py::test_build_thousand_g_and_cadd tests/adapter/test_query.py::test_build_clinsig tests/adapter/test_query.py::test_build_clinsig_filter tests/adapter/test_query.py::test_build_clinsig_always tests/adapter/test_query.py::test_build_clinsig_always_only tests/adapter/test_query.py::test_build_chrom tests/adapter/test_query.py::test_build_range
scout/adapter/mongo/query.py scout/server/blueprints/variants/templates/variants/sv-variant.html scout/server/blueprints/variants/forms.py scout/server/blueprints/variants/templates/variants/sv-variants.html
scout/adapter/mongo/query.py scout/server/blueprints/variants/templates/variants/sv-variant.html scout/server/blueprints/variants/forms.py scout/server/blueprints/variants/templates/variants/sv-variants.html