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dbVar

Database of genomic structural variation

nsv4685890

Organism: Homo sapiens

Study:nstd102 (Clinical Structural Variants)
Variant Type:copy number variation
Method Type:Multiple
Submitted on:GRCh37

Variant Calls:1
Validation:Not tested
Clinical Assertions: Yes
Region Size:41,023

Description:NM_000251.3(MSH2):c.(1276+1_1277-1)_(1661+1_16
62-1)del AND Lynch syndrome
Publication(s):ACMG Board of Directors et al. 2014, Church et al. 2001, Giardiello et al. 2014, Goggins et al. 2020, Goldberg et al. 2019, Green et al. 2013, Hegde et al. 2013, Kalia et al. 2016, Kohlmann et al. 2004, Lu et al. 2014, Menko et al. 2013, Mork et al. 2015, No authors et al. 2020, No authors et al. 2021, No authors et al. 2021, Robson et al. 2015, Seppälä et al. 2021, Stoffel et al. 2014, Syngal et al. 2015, Trepanier et al. 2004, Vasen et al. 2013

Links to Other Resources

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: 242 SVs from 32 studies. See in: genome view

Remapped(Score: Perfect):47,429,942-47,470,964

Variant Region Placement Information

Variant Region ID	Placement Type	Score	Assembly	Assembly Unit	Reciprocity	Sequence ID	Chr	Outer Start	Inner Start	Inner Stop	Outer Stop
nsv4685890	Remapped	Perfect	GRCh38.p12	Primary Assembly	First Pass	NC_000002.12	Chr2	47,429,942	47,445,547	47,466,809	47,470,964
nsv4685890	Submitted genomic		GRCh37 (hg19)	Primary Assembly		NC_000002.11	Chr2	47,657,081	47,672,686	47,693,948	47,698,103

Variant Call Information

Variant Call ID	Type	Method	Analysis	Subject Phenotype	Clinical Interpretation	Source of Interpretation	ClinVar ID
nssv16216858	deletion	Multiple	Multiple	Lynch Syndrome; Lynch syndrome	Pathogenic	ClinVar	RCV000076109.5, VCV000090613.4

Variant Call Placement Information

Variant Call ID	Placement Type	Score	HGVS	Assembly	Reciprocity	Sequence ID	Chr	Outer Start	Inner Start	Inner Stop	Outer Stop
nssv16216858	Remapped	Perfect	NC_000002.12:g.(47 429942_47445547)_( 47466809_47470964) del	GRCh38.p12	First Pass	NC_000002.12	Chr2	47,429,942	47,445,547	47,466,809	47,470,964
nssv16216858	Submitted genomic		NC_000002.11:g.(47 657081_47672686)_( 47693948_47698103) del	GRCh37 (hg19)		NC_000002.11	Chr2	47,657,081	47,672,686	47,693,948	47,698,103

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
nssv16216858	GRCh37: NC_000002.11:g.(47657081_47672686)_(47693948_47698103)del	deletion	see ClinVar for details	Lynch Syndrome; Lynch syndrome	Pathogenic	ClinVar	RCV000076109.5, VCV000090613.4

No genotype data were submitted for this variant

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