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NM_000742.4(CHRNA2):c.745G>A (p.Ala249Thr)

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Interpretation:
Conflicting interpretations of pathogenicity​

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

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Sep 24, 2021)
Last evaluated:
Dec 18, 2020
Accession:
VCV000204946.7
Variation ID:
204946
Description:
single nucleotide variant
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NM_000742.4(CHRNA2):c.745G>A (p.Ala249Thr)

Allele ID
202240
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
8p21.2
Genomic location
8: 27463698 (GRCh38) GRCh38 UCSC
8: 27321215 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000008.10:g.27321215C>T
NC_000008.11:g.27463698C>T
NG_015827.1:g.20599G>A
... more HGVS
Protein change
A249T, A234T, A51T, A90T
Other names
p.A249T:GCC>ACC
Canonical SPDI
NC_000008.11:27463697:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00060 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00024
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Exome Aggregation Consortium (ExAC) 0.00023
The Genome Aggregation Database (gnomAD), exomes 0.00022
The Genome Aggregation Database (gnomAD) 0.00029
1000 Genomes Project 0.00060
Links
ClinGen: CA313415
dbSNP: rs77710085
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 12, 2018 RCV000407778.2
Likely benign 1 criteria provided, single submitter Nov 3, 2020 RCV001081783.2
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Dec 18, 2020 RCV000711162.6
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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
(Mar 05, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000841492.1
Submitted: (Aug 31, 2018)
Evidence details
Uncertain significance
(Nov 22, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000702786.2
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: SCV000473190.3
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
(Nov 03, 2020)
criteria provided, single submitter
Method: clinical testing
Autosomal dominant nocturnal frontal lobe epilepsy
Allele origin: germline
Invitae
Accession: SCV000562073.6
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Dec 18, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000240422.7
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 rs77710085...

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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