NM_000081.4(LYST):c.11268-5del AND not provided

Germline classification:: Benign (3 submissions)
Last evaluated:: Aug 22, 2019
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001573976.4

Allele description [Variation Report for NM_000081.4(LYST):c.11268-5del]

NM_000081.4(LYST):c.11268-5del

Gene:

LYST:lysosomal trafficking regulator [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

1q42.3

Genomic location:

Preferred name:

NM_000081.4(LYST):c.11268-5del

HGVS:

NC_000001.10:g.235826383del
NC_000001.11:g.235663095del
NG_007397.1:g.225558del
NM_000081.4:c.11268-5delMANE SELECT
NM_001301365.1:c.11268-5del
LRG_143t1:c.11268-6del
LRG_143t2:c.11268-5del
LRG_143:g.225558del
NC_000001.10:g.235826383del
NC_000001.10:g.235826383delA
NC_000001.10:g.235826395del
NC_000001.10:g.235826395del
NC_000001.11:g.235663095del
NM_000081.3:c.11268-5delT
NM_000081.3:c.11268-6delT
NM_001301365.1:c.11268-5delT

Links:

dbSNP: rs36014994

NCBI 1000 Genomes Browser:

rs36014994

Molecular consequence:

NM_000081.4:c.11268-5del - intron variant - [Sequence Ontology: SO:0001627]
NM_001301365.1:c.11268-5del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Normal ovarian and fallopian tube epithelial cells immortalized with hTERT
Normal ovarian and fallopian tube epithelial cells immortalized with hTERT
Accession: GDS5321

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001800616	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus	no assertion criteria provided	Likely benign	germline	clinical testing
SCV001871643	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Aug 22, 2019)	germline	clinical testing	Citation Link,
SCV002074692	GenomeConnect, ClinGen	no classification provided	not provided	unknown	phenotyping only

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001800616

Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus

no assertion criteria provided

Likely benign

germline

clinical testing

SCV001871643

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Benign
(Aug 22, 2019)

germline

clinical testing

Citation Link,

SCV002074692

GenomeConnect, ClinGen

no classification provided

not provided

unknown

phenotyping only

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	phenotyping only

Details of each submission

From Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus, SCV001800616.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GeneDx, SCV001871643.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This variant is associated with the following publications: (PMID: 27781387, 29357941)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GenomeConnect, ClinGen, SCV002074692.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	phenotyping only	not provided

Description

Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 15, 2024

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