rs1316971
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000261751.8(CHRNB4):c.56-2581T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 152,090 control chromosomes in the GnomAD database, including 32,376 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 0.62 ( 32376 hom., cov: 33)
Consequence
CHRNB4
ENST00000261751.8 intron
ENST00000261751.8 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.502
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=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHRNB4 | NM_000750.5 | c.56-2581T>C | intron_variant | ENST00000261751.8 | NP_000741.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHRNB4 | ENST00000261751.8 | c.56-2581T>C | intron_variant | 1 | NM_000750.5 | ENSP00000261751 | P1 | |||
CHRNB4 | ENST00000412074.6 | c.56-2581T>C | intron_variant | 1 | ENSP00000416386 | |||||
CHRNB4 | ENST00000559849.5 | c.47-2581T>C | intron_variant, NMD_transcript_variant | 1 | ENSP00000457404 | |||||
CHRNB4 | ENST00000560511.5 | n.410-2581T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.619 AC: 94123AN: 151972Hom.: 32370 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.619 AC: 94161AN: 152090Hom.: 32376 Cov.: 33 AF XY: 0.611 AC XY: 45456AN XY: 74352
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at