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NM_152594.3(SPRED1):c.939G>A (p.Thr313=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
7 (Most recent: Sep 30, 2021)
Last evaluated:
Nov 12, 2020
Accession:
VCV000241992.9
Variation ID:
241992
Description:
single nucleotide variant
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NM_152594.3(SPRED1):c.939G>A (p.Thr313=)

Allele ID
242035
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
15q14
Genomic location
15: 38351268 (GRCh38) GRCh38 UCSC
15: 38643469 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000015.10:g.38351268G>A
NC_000015.9:g.38643469G>A
NG_008980.1:g.103418G>A
NM_152594.3:c.939G>A MANE Select NP_689807.1:p.Thr313= synonymous
Protein change
-
Other names
-
Canonical SPDI
NC_000015.10:38351267:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00060 (A)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00070
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00046
Trans-Omics for Precision Medicine (TOPMed) 0.00049
1000 Genomes Project 0.00060
Links
ClinGen: CA7470207
dbSNP: rs140644874
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 Jul 31, 2020 RCV000588514.6
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Nov 12, 2020 RCV001079971.3
Benign 2 criteria provided, single submitter Nov 14, 2017 RCV000434497.5
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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
(Nov 12, 2020)
criteria provided, single submitter
Method: clinical testing
Legius syndrome
Allele origin: germline
Invitae
Accession: SCV000291526.7
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Jul 31, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000520807.6
Submitted: (Jul 20, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 28150585)
Benign
(Apr 18, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000699964.1
Submitted: (Jan 25, 2018)
Evidence details
Comment:
Variant summary: The SPRED1 c.939G>A (p.Thr313Thr) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a … (more)
Benign
(Nov 14, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000710934.2
Submitted: (Mar 21, 2019)
Evidence details
Comment:
p.Thr313Thr in exon 7 of SPRED1: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue, … (more)
Likely benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Legius syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001274828.1
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
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Clinical Genetics,Academic Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001923398.1
Submitted: (Sep 23, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Human Genetics - Radboudumc,Radboudumc
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001955794.1
Submitted: (Sep 30, 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 rs140644874...

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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