nsv3890003
- Organism: Homo sapiens
- Study:nstd102 (Clinical Structural Variants)
- Variant Type:copy number variation
- Method Type:Multiple
- Submitted on:GRCh38
- Variant Calls:2
- Validation:Not tested
- Clinical Assertions: Yes
- Region Size:120
- Description:
See descriptions for individual calls in download files - Publication(s):ACMG Board of Directors et al. 2014, Civeira et al. 2004, Cuchel et al. 2014, Feldman et al. 2015, Goldberg et al. 2011, Green et al. 2013, Kalia et al. 2016, Miller et al. 2021, Miller et al. 2022, Mysliwiec et al. 2014, Rynkiewicz et al. 2013, Sullivan et al. 2012, Watts et al. 2013, Youngblom et al. 2014
- ClinVar: RCV000459722.2
- ClinVar: RCV003318757.1
- ClinVar: VCV000417370.2
- ClinVar: VCV002574175.1
- GeneReviews: NBK174884
- MONDO: 0007750
- MedGen: C0745103
- OMIM: 143890
- OMIM: 144400
- OMIM: 600946.0028
- Orphanet: 391665
- PubMed: 15177124
- PubMed: 21600525
- PubMed: 22364837
- PubMed: 23725921
- PubMed: 23788249
- PubMed: 24404629
- PubMed: 24418289
- PubMed: 24636176
- PubMed: 25053660
- PubMed: 25356965
- PubMed: 25404096
- PubMed: 27854360
- PubMed: 34012068
- PubMed: 35802134
- Overlapping Genes
Source: NCBI
- Genome View
- Variant Region Details and Evidence
- Validation Information
- Clinical Assertions
- Genotype Information
Genome View
Select assembly:Overlapping variant regions from other studies: 80 SVs from 20 studies. See in: genome view
Overlapping variant regions from other studies: 80 SVs from 20 studies. See in: genome view
Variant Region Placement Information
| Variant Region ID | Placement Type | Score | Assembly | Assembly Unit | Reciprocity | Sequence ID | Chr | Inner Start | Inner Stop |
|---|---|---|---|---|---|---|---|---|---|
| nsv3890003 | Submitted genomic | GRCh38 (hg38) | Primary Assembly | NC_000019.10 | Chr19 | 11,110,652 | 11,110,771 | ||
| nsv3890003 | Remapped | Perfect | GRCh37.p13 | Primary Assembly | First Pass | NC_000019.9 | Chr19 | 11,221,328 | 11,221,447 |
Variant Call Information
| Variant Call ID | Type | Method | Analysis | Subject Phenotype | Clinical Interpretation | Source of Interpretation | ClinVar ID |
|---|---|---|---|---|---|---|---|
| nssv15129823 | deletion | Multiple | Multiple | Familial Hypercholesterolemia; Familial hypercholesterolemia; HYPERCHOLESTEROLEMIA, FAMILIAL; Homozygous familial hypercholesterolemia; MOVED TO 143890; See individual phenotypes in OMIM allelic variants | Conflicting interpretations of pathogenicity | ClinVar | RCV000459722.2, VCV000417370.2 |
| nssv18830993 | deletion | Multiple | Multiple | Familial Hypercholesterolemia; Familial hypercholesterolemia; HYPERCHOLESTEROLEMIA, FAMILIAL; Homozygous familial hypercholesterolemia; MOVED TO 143890; See individual phenotypes in OMIM allelic variants | Pathogenic | ClinVar | RCV003318757.1, VCV002574175.1 |
Variant Call Placement Information
| Variant Call ID | Placement Type | Score | HGVS | Assembly | Reciprocity | Sequence ID | Chr | Inner Start | Inner Stop |
|---|---|---|---|---|---|---|---|---|---|
| nssv15129823 | Submitted genomic | NC_000019.10:g.(?_ 11110652)_(1111077 1_?)del | GRCh38 (hg38) | NC_000019.10 | Chr19 | 11,110,652 | 11,110,771 | ||
| nssv18830993 | Submitted genomic | NC_000019.10:g.(?_ 11110652)_(1111077 1_?)del | GRCh38 (hg38) | NC_000019.10 | Chr19 | 11,110,652 | 11,110,771 | ||
| nssv18830993 | Remapped | Perfect | NC_000019.9:g.(?_1 1221328)_(11221447 _?)del | GRCh37.p13 | First Pass | NC_000019.9 | Chr19 | 11,221,328 | 11,221,447 |
| nssv15129823 | Submitted genomic | NC_000019.9:g.(?_1 1221328)_(11221447 _?)del | GRCh37 (hg19) | NC_000019.9 | Chr19 | 11,221,328 | 11,221,447 |
No validation data were submitted for this variant
Clinical Assertions There exist variant calls with the same type and copy number with different clinical interpretation.
| Variant Call ID | HGVS | Type | Allele Origin | Subject Phenotype | Clinical Interpretation | Source of Interpretation | ClinVar ID |
|---|---|---|---|---|---|---|---|
| nssv15129823 | GRCh37: NC_000019.9:g.(?_11221328)_(11221447_?)del, GRCh38: NC_000019.10:g.(?_11110652)_(11110771_?)del | deletion | germline | Familial Hypercholesterolemia; Familial hypercholesterolemia; HYPERCHOLESTEROLEMIA, FAMILIAL; Homozygous familial hypercholesterolemia; MOVED TO 143890; See individual phenotypes in OMIM allelic variants | Conflicting interpretations of pathogenicity | ClinVar | RCV000459722.2, VCV000417370.2 |
| nssv18830993 | GRCh38: NC_000019.10:g.(?_11110652)_(11110771_?)del | deletion | germline | Familial Hypercholesterolemia; Familial hypercholesterolemia; HYPERCHOLESTEROLEMIA, FAMILIAL; Homozygous familial hypercholesterolemia; MOVED TO 143890; See individual phenotypes in OMIM allelic variants | Pathogenic | ClinVar | RCV003318757.1, VCV002574175.1 |