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GeneBe

rs684513

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000745.4(CHRNA5):c.106+233C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,056 control chromosomes in the GnomAD database, including 4,489 homozygotes. 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 0.23 ( 4489 hom., cov: 31)

Consequence

CHRNA5
NM_000745.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0190
Variant links:
Genes affected
CHRNA5 (HGNC:1959): (cholinergic receptor nicotinic alpha 5 subunit) The protein encoded by this gene is a nicotinic acetylcholine receptor subunit and a member of a superfamily of ligand-gated ion channels that mediate fast signal transmission at synapses. These receptors are thought to be heteropentamers composed of separate but similar subunits. Defects in this gene have been linked to susceptibility to lung cancer type 2 (LNCR2).[provided by RefSeq, Jun 2010]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CHRNA5NM_000745.4 linkuse as main transcriptc.106+233C>G intron_variant ENST00000299565.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CHRNA5ENST00000299565.9 linkuse as main transcriptc.106+233C>G intron_variant 1 NM_000745.4 P1
CHRNA5ENST00000559554.5 linkuse as main transcriptc.106+233C>G intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.231
AC:
35079
AN:
151938
Hom.:
4475
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.196
Gnomad AMI
AF:
0.120
Gnomad AMR
AF:
0.395
Gnomad ASJ
AF:
0.198
Gnomad EAS
AF:
0.235
Gnomad SAS
AF:
0.368
Gnomad FIN
AF:
0.230
Gnomad MID
AF:
0.278
Gnomad NFE
AF:
0.208
Gnomad OTH
AF:
0.239
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.231
AC:
35117
AN:
152056
Hom.:
4489
Cov.:
31
AF XY:
0.237
AC XY:
17628
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.195
Gnomad4 AMR
AF:
0.395
Gnomad4 ASJ
AF:
0.198
Gnomad4 EAS
AF:
0.235
Gnomad4 SAS
AF:
0.367
Gnomad4 FIN
AF:
0.230
Gnomad4 NFE
AF:
0.208
Gnomad4 OTH
AF:
0.243
Alfa
AF:
0.107
Hom.:
159
Bravo
AF:
0.239
Asia WGS
AF:
0.305
AC:
1061
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
Cadd
Benign
5.2
Dann
Benign
0.54

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs684513; hg19: chr15-78858400; API