nsv5564335
- Organism: Homo sapiens
- Study:nstd102 (Clinical Structural Variants)
- Variant Type:copy number variation
- Method Type:Multiple
- Submitted on:GRCh37, GRCh38
- Variant Calls:1
- Validation:Not tested
- Clinical Assertions: Yes
- Region Size:121
- Description:NM_000179.3(MSH6):c.3439-2_3556+1del AND Carcinoma of colon
- Publication(s):Duffy et al. 2013, Evaluation of Genomic Applications in Practice and Prevention (EGAPP) Working Group et al. 2013, Febbo et al. 2011, García-Alfonso et al. 2012, García-Alfonso et al. 2015, García-Alfonso et al. 2020, Imperiale et al. 2014, Kohlmann et al. 2004, Locker et al. 2006, Schmoll et al. 2012, Seppälä et al. 2021, Sturgeon et al. 2008, Wong et al. 2014
- ClinVar: RCV001356831.1
- ClinVar: VCV001050027.1
- GeneReviews: NBK1211
- MONDO: 0002032
- MedGen: C0699790
- PubMed: 17060676
- PubMed: 19042984
- PubMed: 20301390
- PubMed: 22138009
- PubMed: 22855150
- PubMed: 23012255
- PubMed: 23429431
- PubMed: 23852704
- PubMed: 24996433
- PubMed: 25006736
- PubMed: 25373533
- PubMed: 32418154
- PubMed: 34043773
- 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: 108 SVs from 17 studies. See in: genome view
Overlapping variant regions from other studies: 108 SVs from 17 studies. See in: genome view
Variant Region Placement Information
| Variant Region ID | Placement Type | Assembly | Assembly Unit | Sequence ID | Chr | Start | Stop |
|---|---|---|---|---|---|---|---|
| nsv5564335 | Submitted genomic | GRCh38 (hg38) | Primary Assembly | NC_000002.12 | Chr2 | 47,804,908 | 47,805,028 |
| nsv5564335 | Submitted genomic | GRCh37 (hg19) | Primary Assembly | NC_000002.11 | Chr2 | 48,032,047 | 48,032,167 |
Variant Call Information
| Variant Call ID | Type | Method | Analysis | Subject Phenotype | Clinical Interpretation | Source of Interpretation | ClinVar ID |
|---|---|---|---|---|---|---|---|
| nssv17059400 | deletion | Multiple | Multiple | Carcinoma of colon; Lynch Syndrome | Pathogenic | ClinVar | RCV001356831.1, VCV001050027.1 |
Variant Call Placement Information
| Variant Call ID | Placement Type | HGVS | Assembly | Sequence ID | Chr | Start | Stop |
|---|---|---|---|---|---|---|---|
| nssv17059400 | Submitted genomic | NC_000002.12:g.478 04908_47805028del | GRCh38 (hg38) | NC_000002.12 | Chr2 | 47,804,908 | 47,805,028 |
| nssv17059400 | Submitted genomic | NC_000002.11:g.480 32047_48032167del | GRCh37 (hg19) | NC_000002.11 | Chr2 | 48,032,047 | 48,032,167 |
No validation data were submitted for this variant
Clinical Assertions
| Variant Call ID | HGVS | Type | Allele Origin | Subject Phenotype | Clinical Interpretation | Source of Interpretation | ClinVar ID |
|---|---|---|---|---|---|---|---|
| nssv17059400 | GRCh37: NC_000002.11:g.48032047_48032167del, GRCh38: NC_000002.12:g.47804908_47805028del | deletion | unknown | Carcinoma of colon; Lynch Syndrome | Pathogenic | ClinVar | RCV001356831.1, VCV001050027.1 |