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NM_000742.4(CHRNA2):c.1530C>T (p.Ile510=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(3);Likely benign(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Sep 24, 2021)
Last evaluated:
Nov 20, 2020
Accession:
VCV000362693.8
Variation ID:
362693
Description:
single nucleotide variant
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NM_000742.4(CHRNA2):c.1530C>T (p.Ile510=)

Allele ID
308761
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
8p21.2
Genomic location
8: 27461689 (GRCh38) GRCh38 UCSC
8: 27319206 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000008.10:g.27319206G>A
NC_000008.11:g.27461689G>A
NG_015827.1:g.22608C>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000008.11:27461688:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00040 (A)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00041
Trans-Omics for Precision Medicine (TOPMed) 0.00048
Exome Aggregation Consortium (ExAC) 0.00035
The Genome Aggregation Database (gnomAD) 0.00046
Trans-Omics for Precision Medicine (TOPMed) 0.00047
1000 Genomes Project 0.00040
The Genome Aggregation Database (gnomAD) 0.00051
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00054
Links
ClinGen: CA4689410
dbSNP: rs149142237
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000341306.2
Likely benign 1 criteria provided, single submitter Apr 8, 2017 RCV000720761.1
Benign 1 criteria provided, single submitter Apr 11, 2017 RCV000438533.4
Likely benign 1 criteria provided, single submitter Nov 20, 2020 RCV001079388.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Nov 12, 2018 RCV000733010.4
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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

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Apr 11, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000612734.1
Submitted: (Aug 17, 2017)
Evidence details
Uncertain significance
(May 18, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000861019.1
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Epilepsy, nocturnal frontal lobe, type 4
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000473180.3
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
(Apr 08, 2017)
criteria provided, single submitter
Method: clinical testing
Seizures
Allele origin: germline
Ambry Genetics
Accession: SCV000851642.2
Submitted: (Nov 30, 2020)
Evidence details
Comment:
Synonymous alterations with insufficient evidence to classify as benign
Likely benign
(Nov 20, 2020)
criteria provided, single submitter
Method: clinical testing
Autosomal dominant nocturnal frontal lobe epilepsy
Allele origin: germline
Invitae
Accession: SCV000562070.6
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Nov 12, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000512604.4
Submitted: (Sep 24, 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=CHRNA2 - - - -

Text-mined citations for rs149142237...

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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