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NM_001130438.3(SPTAN1):c.5460G>A (p.Ala1820=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 27, 2020
Accession:
VCV000139299.5
Variation ID:
139299
Description:
single nucleotide variant
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NM_001130438.3(SPTAN1):c.5460G>A (p.Ala1820=)

Allele ID
143002
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9q34.11
Genomic location
9: 128617742 (GRCh38) GRCh38 UCSC
9: 131380021 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000009.11:g.131380021G>A
NC_000009.12:g.128617742G>A
NG_027748.1:g.70185G>A
... more HGVS
Protein change
-
Other names
p.A1820A:GCG>GCA
Canonical SPDI
NC_000009.12:128617741:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00080 (A)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00039
Trans-Omics for Precision Medicine (TOPMed) 0.00165
The Genome Aggregation Database (gnomAD) 0.00178
1000 Genomes Project 0.00080
Trans-Omics for Precision Medicine (TOPMed) 0.00157
The Genome Aggregation Database (gnomAD) 0.00161
Exome Aggregation Consortium (ExAC) 0.00055
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00161
Links
ClinGen: CA302996
dbSNP: rs140191388
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 2 criteria provided, multiple submitters, no conflicts Mar 13, 2015 RCV000178486.3
Benign 1 criteria provided, single submitter Nov 21, 2018 RCV000555111.4
Benign 1 criteria provided, single submitter Nov 27, 2020 RCV001084995.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SPTAN1 - - GRCh38
GRCh37
1291 1339

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Oct 04, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000171852.12
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
(Mar 13, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000230573.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Nov 21, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV001145805.1
Submitted: (Sep 25, 2019)
Evidence details
Benign
(Nov 27, 2020)
criteria provided, single submitter
Method: clinical testing
Early infantile epileptic encephalopathy with suppression bursts
Allele origin: germline
Invitae
Accession: SCV000633784.4
Submitted: (Jan 07, 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
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=SPTAN1 - - - -

Text-mined citations for rs140191388...

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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