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NM_001130438.3(SPTAN1):c.5775C>T (p.Thr1925=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 8, 2020
Accession:
VCV000139303.6
Variation ID:
139303
Description:
single nucleotide variant
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NM_001130438.3(SPTAN1):c.5775C>T (p.Thr1925=)

Allele ID
143006
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9q34.11
Genomic location
9: 128621199 (GRCh38) GRCh38 UCSC
9: 131383478 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000009.11:g.131383478C>T
NC_000009.12:g.128621199C>T
NM_001130438.3:c.5775C>T MANE Select NP_001123910.1:p.Thr1925= synonymous
... more HGVS
Protein change
-
Other names
p.T1925T:ACC>ACT
Canonical SPDI
NC_000009.12:128621198:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00080 (T)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00086
The Genome Aggregation Database (gnomAD) 0.00080
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00138
Trans-Omics for Precision Medicine (TOPMed) 0.00116
Exome Aggregation Consortium (ExAC) 0.00075
1000 Genomes Project 0.00080
Links
ClinGen: CA293745
dbSNP: rs140353002
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 Oct 13, 2016 RCV000128264.4
Benign 1 criteria provided, single submitter Dec 8, 2020 RCV000462041.6
Likely benign 1 criteria provided, single submitter Sep 6, 2016 RCV000716939.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SPTAN1 - - GRCh38
GRCh37
1284 1332

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Oct 13, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000615447.1
Submitted: (Aug 17, 2017)
Evidence details
Likely benign
(Jul 01, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000342660.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Dec 08, 2020)
criteria provided, single submitter
Method: clinical testing
Early infantile epileptic encephalopathy with suppression bursts
Allele origin: germline
Invitae
Accession: SCV000562992.6
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Mar 04, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000171856.12
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)
Likely benign
(Sep 06, 2016)
criteria provided, single submitter
Method: clinical testing
Seizures
Allele origin: germline
Ambry Genetics
Accession: SCV000847784.2
Submitted: (Nov 30, 2020)
Evidence details
Comment:
Synonymous alterations with insufficient evidence to classify as benign

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
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=SPTAN1 - - - -

Text-mined citations for rs140353002...

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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 Jun 14, 2021