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NM_012431.3(SEMA3E):c.2152G>A (p.Gly718Ser)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
2 (Most recent: Jul 14, 2021)
Last evaluated:
Dec 3, 2019
Accession:
VCV000459538.5
Variation ID:
459538
Description:
single nucleotide variant
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NM_012431.3(SEMA3E):c.2152G>A (p.Gly718Ser)

Allele ID
456960
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7q21.11
Genomic location
7: 83367762 (GRCh38) GRCh38 UCSC
7: 82997078 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000007.13:g.82997078C>T
NC_000007.14:g.83367762C>T
NG_021242.2:g.286402G>A
... more HGVS
Protein change
G718S, G658S
Other names
-
Canonical SPDI
NC_000007.14:83367761:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00010
The Genome Aggregation Database (gnomAD), exomes 0.00011
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00023
Trans-Omics for Precision Medicine (TOPMed) 0.00012
Exome Aggregation Consortium (ExAC) 0.00016
Links
ClinGen: CA4321816
dbSNP: rs148649507
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Dec 3, 2019 RCV000559199.3
Likely benign 1 criteria provided, single submitter Feb 5, 2019 RCV001534140.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SEMA3E - - GRCh38
GRCh37
318 337

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Dec 03, 2019)
criteria provided, single submitter
Method: clinical testing
CHARGE association
Allele origin: germline
Invitae
Accession: SCV000631234.4
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change replaces glycine with serine at codon 718 of the SEMA3E protein (p.Gly718Ser). The glycine residue is moderately conserved and there is a … (more)
Likely benign
(Feb 05, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001751040.1
Submitted: (Jul 14, 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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Title Author Journal Year Link
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532

Text-mined citations for rs148649507...

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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 Oct 30, 2021