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NM_152594.3(SPRED1):c.583-7A>G

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
9 (Most recent: Sep 30, 2021)
Last evaluated:
Dec 3, 2020
Accession:
VCV000047969.10
Variation ID:
47969
Description:
single nucleotide variant
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NM_152594.3(SPRED1):c.583-7A>G

Allele ID
57133
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
15q14
Genomic location
15: 38349415 (GRCh38) GRCh38 UCSC
15: 38641616 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000015.10:g.38349415A>G
NC_000015.9:g.38641616A>G
NG_008980.1:g.101565A>G
NM_152594.3:c.583-7A>G MANE Select
Protein change
-
Other names
-
Canonical SPDI
NC_000015.10:38349414:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.01058 (G)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00785
The Genome Aggregation Database (gnomAD) 0.00561
Trans-Omics for Precision Medicine (TOPMed) 0.00689
Exome Aggregation Consortium (ExAC) 0.00211
The Genome Aggregation Database (gnomAD), exomes 0.00166
The Genome Aggregation Database (gnomAD) 0.00630
1000 Genomes Project 0.01058
Trans-Omics for Precision Medicine (TOPMed) 0.00668
Links
ClinGen: CA142280
dbSNP: rs115970207
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 5 criteria provided, multiple submitters, no conflicts Feb 2, 2017 RCV000041244.7
Benign 3 criteria provided, multiple submitters, no conflicts Dec 3, 2020 RCV000206311.11
Benign 1 criteria provided, single submitter Apr 17, 2017 RCV000590597.3
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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
(Mar 19, 2012)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000064935.6
Submitted: (Mar 21, 2019)
Evidence details
Comment:
c.583-7A>G in Intron 05 of SPRED1: This variant is not expected to have clinical significance because it has been identified in 2.4% (88/3738) of African … (more)
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Legius syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000390791.3
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
(Dec 03, 2020)
criteria provided, single submitter
Method: clinical testing
Legius syndrome
Allele origin: germline
Invitae
Accession: SCV000260565.8
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000316212.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Apr 17, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000699962.1
Submitted: (Jan 25, 2018)
Evidence details
Comment:
Variant summary: The SPRED1 c.583-7A>G variant involves the alteration of a non-conserved intronic nucleotide. 5/5 splice prediction tools predict no significant impact on normal splicing. … (more)
Benign
(Jan 21, 2020)
criteria provided, single submitter
Method: clinical testing
Legius syndrome
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV001472996.1
Submitted: (Dec 11, 2020)
Evidence details
Benign
(Feb 02, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000729623.1
Submitted: (Mar 26, 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)
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Human Genetics - Radboudumc,Radboudumc
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001958583.1
Submitted: (Sep 30, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001975589.1
Submitted: (Sep 21, 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 rs115970207...

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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