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NM_001130438.3(SPTAN1):c.6660C>T (p.Asn2220=)

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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:
Nov 18, 2020
Accession:
VCV000139311.8
Variation ID:
139311
Description:
single nucleotide variant
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NM_001130438.3(SPTAN1):c.6660C>T (p.Asn2220=)

Allele ID
143014
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9q34.11
Genomic location
9: 128627469 (GRCh38) GRCh38 UCSC
9: 131389748 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000009.11:g.131389748C>T
NC_000009.12:g.128627469C>T
NG_027748.1:g.79912C>T
... more HGVS
Protein change
-
Other names
p.N2220N:AAC>AAT
Canonical SPDI
NC_000009.12:128627468:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00759 (T)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00596
The Genome Aggregation Database (gnomAD), exomes 0.00136
Trans-Omics for Precision Medicine (TOPMed) 0.00638
1000 Genomes Project 0.00759
Exome Aggregation Consortium (ExAC) 0.00283
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00635
Links
ClinGen: CA295190
dbSNP: rs112955915
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 Feb 7, 2013 RCV000147651.4
Benign 1 criteria provided, single submitter Mar 18, 2016 RCV000716555.1
Benign 1 criteria provided, single submitter Aug 8, 2018 RCV000713522.4
Benign 1 criteria provided, single submitter Nov 18, 2020 RCV001080420.2
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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
1284 1332

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Sep 07, 2012)
criteria provided, single submitter
Method: clinical testing
not specified
(Autosomal dominant inheritance)
Allele origin: germline
Genetic Services Laboratory,University of Chicago
Accession: SCV000195100.1
Submitted: (Sep 11, 2014)
Comment:
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated … (more)
Evidence details
Benign
(Feb 07, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000171864.12
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)
Benign
(Aug 08, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000844144.1
Submitted: (Aug 31, 2018)
Evidence details
Benign
(Mar 18, 2016)
criteria provided, single submitter
Method: clinical testing
Seizures
Allele origin: germline
Ambry Genetics
Accession: SCV000847396.2
Submitted: (Nov 30, 2020)
Evidence details
Comment:
Subpopulation frequency in support of benign classification;Synonymous alterations with insufficient evidence to classify as benign
Benign
(Nov 18, 2020)
criteria provided, single submitter
Method: clinical testing
Early infantile epileptic encephalopathy with suppression bursts
Allele origin: germline
Invitae
Accession: SCV000562988.6
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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs112955915...

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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