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NM_001909.5(CTSD):c.294G>A (p.Thr98=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Mar 31, 2021)
Last evaluated:
Feb 17, 2020
Accession:
VCV000137053.4
Variation ID:
137053
Description:
single nucleotide variant
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NM_001909.5(CTSD):c.294G>A (p.Thr98=)

Allele ID
140756
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11p15.5
Genomic location
11: 1759574 (GRCh38) GRCh38 UCSC
11: 1780804 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000011.10:g.1759574C>T
NC_000011.9:g.1780804C>T
NG_008655.1:g.9419G>A
NM_001909.5:c.294G>A MANE Select NP_001900.1:p.Thr98= synonymous
Protein change
-
Other names
p.T98T:ACG>ACA
Canonical SPDI
NC_000011.10:1759573:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00009
The Genome Aggregation Database (gnomAD), exomes 0.00006
Exome Aggregation Consortium (ExAC) 0.00007
The Genome Aggregation Database (gnomAD) 0.00019
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Links
ClinGen: CA290546
dbSNP: rs369373285
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 1 criteria provided, single submitter Sep 26, 2013 RCV000124641.2
Uncertain significance 1 criteria provided, single submitter Feb 17, 2020 RCV000706456.3
Uncertain significance 1 no assertion criteria provided - RCV001355385.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CTSD - - GRCh38
GRCh37
377 410

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Sep 26, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000168074.12
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Uncertain significance
(Feb 17, 2020)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis
Allele origin: germline
Invitae
Accession: SCV000835505.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change affects codon 98 of the CTSD mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid … (more)
Uncertain significance
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: unknown
Department of Pathology and Laboratory Medicine,Sinai Health System
Additional submitter:
Franklin by Genoox
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV001550259.1
Submitted: (Mar 31, 2021)
Evidence details
Comment:
The CTSD p.Thr98Thr variant was not identified in the literature but was identified in dbSNP (ID: rs369373285) and ClinVar (classified as benign by GeneDx and … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532

Text-mined citations for rs369373285...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 08, 2021