Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_000742.4(CHRNA2):c.1500C>T (p.Ile500=)

Help
Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 7, 2020
Accession:
VCV000204950.7
Variation ID:
204950
Description:
single nucleotide variant
Help

NM_000742.4(CHRNA2):c.1500C>T (p.Ile500=)

Allele ID
202222
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
8p21.2
Genomic location
8: 27461719 (GRCh38) GRCh38 UCSC
8: 27319236 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000008.11:g.27461719G>A
NC_000008.10:g.27319236G>A
NM_000742.4:c.1500C>T MANE Select NP_000733.2:p.Ile500= synonymous
... more HGVS
Protein change
-
Other names
p.I500I:ATC>ATT
Canonical SPDI
NC_000008.11:27461718:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00060 (A)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00158
1000 Genomes Project 0.00060
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00185
The Genome Aggregation Database (gnomAD) 0.00115
Exome Aggregation Consortium (ExAC) 0.00048
Links
ClinGen: CA313423
dbSNP: rs143223159
VarSome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 2 criteria provided, multiple submitters, no conflicts Jul 19, 2016 RCV000186855.2
Benign 1 criteria provided, single submitter Jan 12, 2018 RCV000377222.2
Benign 1 criteria provided, single submitter Dec 7, 2020 RCV000654341.4
Likely benign 1 criteria provided, single submitter Oct 18, 2016 RCV000717219.1
Help
Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CHRNA2 - - GRCh38
GRCh37
473 539

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Dec 29, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000240426.11
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
(Jul 19, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000343728.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Epilepsy, nocturnal frontal lobe, type 4
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000473181.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Likely benign
(Oct 18, 2016)
criteria provided, single submitter
Method: clinical testing
Seizures
Allele origin: germline
Ambry Genetics
Accession: SCV000848068.2
Submitted: (Nov 30, 2020)
Evidence details
Comment:
In silico models in agreement (benign);Synonymous alterations with insufficient evidence to classify as benign
Benign
(Dec 07, 2020)
criteria provided, single submitter
Method: clinical testing
Autosomal dominant nocturnal frontal lobe epilepsy
Allele origin: germline
Invitae
Accession: SCV000776231.4
Submitted: (Jan 07, 2021)
Evidence details

Functional evidence

Help
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

Help
Title Author Journal Year Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CHRNA2 - - - -

Text-mined citations for rs143223159...

Help
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