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NM_152594.3(SPRED1):c.*256C>T

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
2 (Most recent: Aug 20, 2021)
Last evaluated:
Jun 16, 2018
Accession:
VCV000315741.5
Variation ID:
315741
Description:
single nucleotide variant
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NM_152594.3(SPRED1):c.*256C>T

Allele ID
338639
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
15q14
Genomic location
15: 38351920 (GRCh38) GRCh38 UCSC
15: 38644121 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000015.10:g.38351920C>T
NC_000015.9:g.38644121C>T
NG_008980.1:g.104070C>T
NM_152594.3:c.*256C>T MANE Select 3 prime UTR
Protein change
-
Other names
-
Canonical SPDI
NC_000015.10:38351919:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00539 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00941
Trans-Omics for Precision Medicine (TOPMed) 0.00886
The Genome Aggregation Database (gnomAD) 0.01411
1000 Genomes Project 0.00539
The Genome Aggregation Database (gnomAD) 0.01162
Links
ClinGen: CA10645793
dbSNP: rs145373657
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 Jan 13, 2018 RCV000309476.2
Likely benign 1 criteria provided, single submitter Jun 16, 2018 RCV001575160.3
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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
413 435

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Legius syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000390800.3
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
(Jun 16, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001802092.1
Submitted: (Aug 20, 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 rs145373657...

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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 Nov 27, 2021