NM_017882.3(CLN6):c.486+8C>T AND not provided

Germline classification:: Benign (4 submissions)
Last evaluated:: Aug 1, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000675962.33

Allele description [Variation Report for NM_017882.3(CLN6):c.486+8C>T]

NM_017882.3(CLN6):c.486+8C>T

Gene:

CLN6:CLN6 transmembrane ER protein [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

15q23

Genomic location:

Preferred name:

NM_017882.3(CLN6):c.486+8C>T

HGVS:

NC_000015.10:g.68211667G>A
NG_008764.2:g.50545C>T
NM_017882.3:c.486+8C>TMANE SELECT
LRG_832t1:c.486+8C>T
LRG_832:g.50545C>T
NC_000015.9:g.68504005G>A
NM_017882.2:c.486+8C>T

Links:

dbSNP: rs149692285

NCBI 1000 Genomes Browser:

rs149692285

Molecular consequence:

NM_017882.3:c.486+8C>T - intron variant - [Sequence Ontology: SO:0001627]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000167769	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Dec 11, 2018)	germline	clinical testing	Citation Link,
SCV000603088	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2024)	Benign (Oct 6, 2023)	germline	clinical testing	Citation Link,
SCV000801691	Mayo Clinic Laboratories, Mayo Clinic	no assertion criteria provided	Likely benign (Jan 5, 2018)	unknown	clinical testing
SCV002545288	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Benign (Aug 1, 2024)	germline	clinical testing	Citation Link

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	25	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	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	clinical testing

Details of each submission

From GeneDx, SCV000167769.14

#	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: 21990111, 27535533)

#	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 ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000603088.4

#	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	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Mayo Clinic Laboratories, Mayo Clinic, SCV000801691.1

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV002545288.16

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	25	not provided	not provided	clinical testing	not provided

Description

CLN6: BP4, BS1, BS2

#	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		25	not provided	not provided	not provided

Last Updated: Nov 10, 2024

ClinVar

Relating variation to medicine

NM_017882.3(CLN6):c.486+8C>T AND not provided

Allele description [Variation Report for NM_017882.3(CLN6):c.486+8C>T]

NM_017882.3(CLN6):c.486+8C>T

Condition(s)

Recent activity

Assertion and evidence details

Summary from all submissions

Details of each submission

From GeneDx, SCV000167769.14

Description

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000603088.4

From Mayo Clinic Laboratories, Mayo Clinic, SCV000801691.1

From CeGaT Center for Human Genetics Tuebingen, SCV002545288.16

Description