rs3735757
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_000742.4(CHRNA2):c.450-87C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000054 in 1,518,470 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000053 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000054 ( 0 hom. )
Consequence
CHRNA2
NM_000742.4 intron
NM_000742.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.02
Genes affected
CHRNA2 (HGNC:1956): (cholinergic receptor nicotinic alpha 2 subunit) Nicotinic acetylcholine receptors (nAChRs) are ligand-gated ion channels formed by a pentameric arrangement of alpha and beta subunits to create distinct muscle and neuronal receptors. Neuronal receptors are found throughout the peripheral and central nervous system where they are involved in fast synaptic transmission. This gene encodes an alpha subunit that is widely expressed in the brain. The proposed structure for nAChR subunits is a conserved N-terminal extracellular domain followed by three conserved transmembrane domains, a variable cytoplasmic loop, a fourth conserved transmembrane domain, and a short C-terminal extracellular region. Mutations in this gene cause autosomal dominant nocturnal frontal lobe epilepsy type 4. Single nucleotide polymorphisms (SNPs) in this gene have been associated with nicotine dependence. [provided by RefSeq, Nov 2009]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BS2
High AC in GnomAd4 at 8 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152040Hom.: 0 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
8
AN:
152040
Hom.:
Cov.:
31
Gnomad AFR
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GnomAD4 exome AF: 0.0000542 AC: 74AN: 1366430Hom.: 0 AF XY: 0.0000514 AC XY: 35AN XY: 680394 show subpopulations
GnomAD4 exome
AF:
AC:
74
AN:
1366430
Hom.:
AF XY:
AC XY:
35
AN XY:
680394
Gnomad4 AFR exome
AF:
AC:
1
AN:
31184
Gnomad4 AMR exome
AF:
AC:
0
AN:
38772
Gnomad4 ASJ exome
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AC:
0
AN:
25162
Gnomad4 EAS exome
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AC:
0
AN:
37140
Gnomad4 SAS exome
AF:
AC:
0
AN:
81346
Gnomad4 FIN exome
AF:
AC:
38
AN:
50484
Gnomad4 NFE exome
AF:
AC:
32
AN:
1041304
Gnomad4 Remaining exome
AF:
AC:
3
AN:
56938
Heterozygous variant carriers
0
4
8
11
15
19
0.00
0.20
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0.95
Allele balance
Exome Het
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Age
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152040Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74254 show subpopulations
GnomAD4 genome
AF:
AC:
8
AN:
152040
Hom.:
Cov.:
31
AF XY:
AC XY:
1
AN XY:
74254
Gnomad4 AFR
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0
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0
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0
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0
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0
Gnomad4 EAS
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0
AN:
0
Gnomad4 SAS
AF:
AC:
0
AN:
0
Gnomad4 FIN
AF:
AC:
0.000377145
AN:
0.000377145
Gnomad4 NFE
AF:
AC:
0.0000588166
AN:
0.0000588166
Gnomad4 OTH
AF:
AC:
0
AN:
0
Heterozygous variant carriers
0
1
1
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2
3
0.00
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Allele balance
Genome Het
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Alfa
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at