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NM_001909.5(CTSD):c.1215C>A (p.Gly405=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
10 (Most recent: Sep 7, 2021)
Last evaluated:
Dec 8, 2020
Accession:
VCV000128872.10
Variation ID:
128872
Description:
single nucleotide variant
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NM_001909.5(CTSD):c.1215C>A (p.Gly405=)

Allele ID
134320
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11p15.5
Genomic location
11: 1753527 (GRCh38) GRCh38 UCSC
11: 1774757 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000011.10:g.1753527G>T
NC_000011.9:g.1774757G>T
NG_008655.1:g.15466C>A
NM_001909.5:c.1215C>A MANE Select NP_001900.1:p.Gly405= synonymous
Protein change
-
Other names
-
Canonical SPDI
NC_000011.10:1753526:G:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00419 (T)

Allele frequency
1000 Genomes Project 0.00419
Trans-Omics for Precision Medicine (TOPMed) 0.01204
The Genome Aggregation Database (gnomAD) 0.01226
Exome Aggregation Consortium (ExAC) 0.01176
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.01354
Links
ClinGen: CA152535
dbSNP: rs138733377
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 3 criteria provided, multiple submitters, no conflicts Jan 13, 2018 RCV000625067.4
Benign 3 criteria provided, single submitter - RCV000116852.5
Benign 1 criteria provided, single submitter Dec 8, 2020 RCV000229710.5
Benign 2 criteria provided, single submitter Mar 3, 2015 RCV000675948.3
Benign 1 criteria provided, single submitter May 15, 2016 RCV000715784.1
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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
(Jul 09, 2015)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis 10
Allele origin: germline
Genome Diagnostics Laboratory, University Medical Center Utrecht
Study: VKGL Data-share Consensus
Accession: SCV000743665.1
Submitted: (Apr 17, 2018)
Evidence details
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis 10
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000369550.3
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)
Benign
(May 15, 2016)
criteria provided, single submitter
Method: clinical testing
Seizures
Allele origin: germline
Ambry Genetics
Accession: SCV000846615.2
Submitted: (Nov 30, 2020)
Evidence details
Comment:
This alteration is classified as benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA … (more)
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000308521.1
Submitted: (Apr 28, 2016)
Evidence details
Likely benign
(Jul 20, 2016)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis 10
Allele origin: germline
Genome Diagnostics Laboratory, Amsterdam University Medical Center
Study: VKGL Data-share Consensus
Accession: SCV000745771.1
Submitted: (Apr 09, 2018)
Evidence details
Benign
(Dec 08, 2020)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis
Allele origin: germline
Invitae
Accession: SCV000287209.5
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Mar 03, 2015)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001833903.1
Submitted: (Sep 07, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
AllHighlyPenetrant
(Autosomal recessive inheritance)
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000150926.2
Submitted: (Jun 27, 2014)
Evidence details
Comment:
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated … (more)
Likely benign
(Apr 25, 2017)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: unknown
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV000801677.1
Submitted: (May 23, 2018)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Genome Diagnostics Laboratory, Amsterdam University Medical Center
Study: VKGL Data-share Consensus
Accession: SCV001808125.1
Submitted: (Aug 24, 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 rs138733377...

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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 Sep 24, 2021