NM_152594.3(SPRED1):c.377-10A>G AND not specified

Germline classification:: Benign/Likely benign (2 submissions)
Last evaluated:: Mar 27, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000041242.7

Allele description [Variation Report for NM_152594.3(SPRED1):c.377-10A>G]

NM_152594.3(SPRED1):c.377-10A>G

Gene:

SPRED1:sprouty related EVH1 domain containing 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

15q14

Genomic location:

Preferred name:

NM_152594.3(SPRED1):c.377-10A>G

HGVS:

NC_000015.10:g.38324753A>G
NG_008980.1:g.76903A>G
NM_152594.3:c.377-10A>GMANE SELECT
NC_000015.9:g.38616954A>G
NM_152594.2:c.377-10A>G
c.377-10A>G

Links:

dbSNP: rs376134678

NCBI 1000 Genomes Browser:

rs376134678

Molecular consequence:

NM_152594.3:c.377-10A>G - intron variant - [Sequence Ontology: SO:0001627]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000064933	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Likely benign (May 23, 2013)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV003922434	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (Mar 27, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000064933

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Likely benign
(May 23, 2013)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV003922434

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Benign
(Mar 27, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	3	2	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000064933.7

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	3	not provided	not provided	clinical testing	PubMed (1)

Description

377-10A>G in intron 3 of SPRED1: This variant has been identified by our labora tory in a proband and an unaffected parent. This variant is located in the 3' sp lice acceptor region but does not affect the invariant -1 and -2 positions. In a ddition, computational tools do not predict altered splicing. This variant has b een identified in 0.05% (2/4392) of African American chromosomes from a large po pulation by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS /). In addition, the adenine nucleotide is not conserved across evolutionary dis tinct species at position 377-10, and several mammals have a guanine at this pos ition. Therefore, the 377-10A>G variant is likely to be benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		3	not provided	2	not provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV003922434.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 28, 2024

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