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NM_001909.5(CTSD):c.90G>A (p.Thr30=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(3);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Sep 28, 2021)
Last evaluated:
Jul 13, 2020
Accession:
VCV000303841.7
Variation ID:
303841
Description:
single nucleotide variant
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NM_001909.5(CTSD):c.90G>A (p.Thr30=)

Allele ID
325740
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11p15.5
Genomic location
11: 1761447 (GRCh38) GRCh38 UCSC
11: 1782677 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000011.10:g.1761447C>T
NC_000011.9:g.1782677C>T
NG_008655.1:g.7546G>A
NM_001909.5:c.90G>A MANE Select NP_001900.1:p.Thr30= synonymous
Protein change
-
Other names
-
Canonical SPDI
NC_000011.10:1761446:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00016
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
The Genome Aggregation Database (gnomAD), exomes 0.00008
Exome Aggregation Consortium (ExAC) 0.00004
Trans-Omics for Precision Medicine (TOPMed) 0.00011
Links
ClinGen: CA5814296
dbSNP: rs368529527
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Jan 13, 2018 RCV000304091.2
Likely benign 1 criteria provided, single submitter Jul 13, 2020 RCV000632764.3
Likely benign 1 criteria provided, single submitter Jan 17, 2017 RCV000718181.1
Likely benign 1 criteria provided, single submitter Mar 5, 2019 RCV001711904.1
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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
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis 10
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000369572.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Likely benign
(Jan 17, 2017)
criteria provided, single submitter
Method: clinical testing
Seizures
Allele origin: germline
Ambry Genetics
Accession: SCV000849043.2
Submitted: (Nov 30, 2020)
Evidence details
Comment:
This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, … (more)
Likely benign
(Jul 13, 2020)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis
Allele origin: germline
Invitae
Accession: SCV000753950.3
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Mar 05, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000512774.5
Submitted: (Sep 28, 2021)
Evidence details

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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs368529527...

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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 16, 2021