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NM_152594.3(SPRED1):c.594T>C (p.Gly198=)

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Interpretation:
Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Jan 7, 2021)
Last evaluated:
Jul 25, 2020
Accession:
VCV000388363.4
Variation ID:
388363
Description:
single nucleotide variant
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NM_152594.3(SPRED1):c.594T>C (p.Gly198=)

Allele ID
374480
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
15q14
Genomic location
15: 38349433 (GRCh38) GRCh38 UCSC
15: 38641634 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000015.10:g.38349433T>C
NC_000015.9:g.38641634T>C
NM_152594.3:c.594T>C MANE Select NP_689807.1:p.Gly198= synonymous
NG_008980.1:g.101583T>C
Protein change
-
Other names
-
Canonical SPDI
NC_000015.10:38349432:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00004
Exome Aggregation Consortium (ExAC) 0.00002
The Genome Aggregation Database (gnomAD), exomes 0.00001
Links
ClinGen: CA7470134
dbSNP: rs756643495
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 2 criteria provided, multiple submitters, no conflicts Jul 12, 2018 RCV000436734.2
Likely benign 1 criteria provided, single submitter Jul 25, 2020 RCV001251326.1
Likely benign 1 criteria provided, single submitter Jul 12, 2018 RCV001506613.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SPRED1 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
403 425

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Aug 02, 2016)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000530657.5
Submitted: (Sep 14, 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)
Likely benign
(Jul 12, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001017661.1
Submitted: (Mar 14, 2019)
Evidence details
Likely benign
(Jul 25, 2020)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001426881.1
Submitted: (Aug 06, 2020)
Evidence details
Likely benign
(Jul 12, 2018)
criteria provided, single submitter
Method: clinical testing
Legius syndrome
Allele origin: germline
Invitae
Accession: SCV001711538.1
Submitted: (Jan 07, 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 rs756643495...

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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 Jun 14, 2021