NM_004937.3(CTNS):c.970+15G>A AND not provided

Germline classification:: Benign (4 submissions)
Last evaluated:: Dec 31, 2018
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:: RCV000590580.16

Allele description [Variation Report for NM_004937.3(CTNS):c.970+15G>A]

NM_004937.3(CTNS):c.970+15G>A

Gene:

CTNS:cystinosin, lysosomal cystine transporter [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17p13.2

Genomic location:

Preferred name:

NM_004937.3(CTNS):c.970+15G>A

HGVS:

NC_000017.11:g.3659990G>A
NG_012489.2:g.28523G>A
NM_001031681.3:c.970+15G>A
NM_001374492.1:c.970+15G>A
NM_001374493.1:c.529+15G>A
NM_001374494.1:c.529+15G>A
NM_001374495.1:c.529+15G>A
NM_001374496.1:c.529+15G>A
NM_004937.3:c.970+15G>AMANE SELECT
NC_000017.10:g.3563284G>A
NM_001031681.2:c.970+15G>A
NM_004937.2:c.970+15G>A

Links:

dbSNP: rs76153698

NCBI 1000 Genomes Browser:

rs76153698

Molecular consequence:

NM_001031681.3:c.970+15G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001374492.1:c.970+15G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001374493.1:c.529+15G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001374494.1:c.529+15G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001374495.1:c.529+15G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001374496.1:c.529+15G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_004937.3:c.970+15G>A - intron variant - [Sequence Ontology: SO:0001627]

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
SCV000698528	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (Jun 5, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] LabCorp Variant Classification Summary - May 2015.docx, Citation Link,
SCV000801410	Mayo Clinic Laboratories, Mayo Clinic	no assertion criteria provided	Benign (Feb 3, 2016)	unknown	clinical testing
SCV001911975	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Dec 31, 2018)	germline	clinical testing	Citation Link,
SCV005252210	Breakthrough Genomics, Breakthrough Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign	germline	not provided	PubMed (1) [See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

Genetic basis of cystinosis in Turkish patients: a single-center experience.

Topaloglu R, Vilboux T, Coskun T, Ozaltin F, Tinloy B, Gunay-Aygun M, Bakkaloglu A, Besbas N, van den Heuvel L, Kleta R, Gahl WA.

Pediatr Nephrol. 2012 Jan;27(1):115-21. doi: 10.1007/s00467-011-1942-6. Epub 2011 Jul 24.

PubMed [citation]

PMID:: 21786142
PMCID:: PMC3501933

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000698528.1

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

Description

Variant summary: The CTNS c.970+15G>A variant involves the alteration of a non-conserved intronic nucleotide at a position not widely known to affect gene splicing. Mutation taster predicts a benign outcome for this variant. This variant was found in 2496/120078 control chromosomes (45 homozygotes) from ExAC at a frequency of 0.0207865, which is approximately 8 times the estimated maximal expected allele frequency of a pathogenic CTNS variant (0.0025), suggesting this variant is likely a benign polymorphism. It is more common in African subpopulation with an allele frequency of 6.5% (674/10238 chromosomes). This variant was found in a cystinosis patient who carried c.140+1G>T in homozygous state, further supporting benign outcome of the variant of interest. In addition, multiple clinical diagnostic laboratories/reputable databases have classified this variant as likely benign/benign. Taken together, this variant is classified as benign.

#	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, SCV000801410.1

#	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 GeneDx, SCV001911975.1

#	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 Breakthrough Genomics, Breakthrough Genomics, SCV005252210.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	not provided	PubMed (1)

#	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

Last Updated: Oct 26, 2024

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