chr15-78643134-T-C

Variant summary

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

The ENST00000559849.5(CHRNB4):​c.46+6245A>G variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 143,750 control chromosomes in the GnomAD database, including 7,523 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 0.31 ( 7523 hom., cov: 32)

Consequence

CHRNB4
ENST00000559849.5 intron, NMD_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.35
Variant links:
Genes affected
CHRNB4 (HGNC:1964): (cholinergic receptor nicotinic beta 4 subunit) This gene is found within a conserved gene cluster and encodes one of the beta subunits of the nicotinic acetylcholine receptor (nAChRs) superfamily which form ligand-gated ion channels with a central pore that forms a cation channel. Neuronal nAChRs are pentameric structures that can be either homomeric or heteromeric, with heteromeric structures containing both alpha and beta subunits. Each subunit contains an extracellular amino terminus and four transmembrane domains. Nicotine is one of the agonists that binds to the receptor. Variants in this gene have been associated with nicotine dependence and lung cancer. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Sep 2017]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CHRNB4XM_011521186.3 linkuse as main transcriptc.46+6245A>G intron_variant XP_011519488.1
CHRNB4XM_011521187.3 linkuse as main transcriptc.46+6245A>G intron_variant XP_011519489.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CHRNB4ENST00000559849.5 linkuse as main transcriptc.46+6245A>G intron_variant, NMD_transcript_variant 1 ENSP00000457404
CHRNB4ENST00000560511.5 linkuse as main transcriptn.409+6245A>G intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.314
AC:
45084
AN:
143650
Hom.:
7526
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.206
Gnomad AMI
AF:
0.400
Gnomad AMR
AF:
0.224
Gnomad ASJ
AF:
0.378
Gnomad EAS
AF:
0.0984
Gnomad SAS
AF:
0.284
Gnomad FIN
AF:
0.336
Gnomad MID
AF:
0.242
Gnomad NFE
AF:
0.398
Gnomad OTH
AF:
0.298
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.314
AC:
45077
AN:
143750
Hom.:
7523
Cov.:
32
AF XY:
0.308
AC XY:
21689
AN XY:
70410
show subpopulations
Gnomad4 AFR
AF:
0.206
Gnomad4 AMR
AF:
0.224
Gnomad4 ASJ
AF:
0.378
Gnomad4 EAS
AF:
0.0981
Gnomad4 SAS
AF:
0.282
Gnomad4 FIN
AF:
0.336
Gnomad4 NFE
AF:
0.398
Gnomad4 OTH
AF:
0.295
Alfa
AF:
0.366
Hom.:
8234
Bravo
AF:
0.277

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.55
CADD
Benign
17
DANN
Benign
0.96

Splicing

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: rs11633223; hg19: chr15-78935476; API