NM_152594.3(SPRED1):c.583-7A>G AND not provided

Clinical significance:Benign (Last evaluated: Apr 17, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_152594.3(SPRED1):c.583-7A>G]


SPRED1:sprouty related EVH1 domain containing 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
  • NC_000015.10:g.38349415A>G
  • NG_008980.1:g.101565A>G
  • NM_152594.3:c.583-7A>GMANE SELECT
  • NC_000015.9:g.38641616A>G
  • NM_152594.2:c.583-7A>G
  • c.583-7A>G
dbSNP: rs115970207
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_152594.3:c.583-7A>G - intron variant - [Sequence Ontology: SO:0001627]


MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000699962Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
(Apr 17, 2017)
germlineclinical testing

LabCorp Variant Classification Summary - May 2015.docx

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000699962.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided


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. This variant was found in 248/117724 control chromosomes (including 4 homozygotes) from ExAC, predominantly observed in the African subpopulation at a frequency of 0.022615 (229/10126). This frequency is about 9046 times the estimated maximal expected allele frequency of a pathogenic SPRED1 variant (0.0000025), therefore this is likely a benign polymorphism found primarily in the populations of African origin. In addition, multiple clinical diagnostic laboratories/reputable databases have classified this variant as benign/likely benign. Taken together, this variant is classified as Benign.

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 10, 2021

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