rs2072660
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000748.3(CHRNB2):c.*313T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 444,814 control chromosomes in the GnomAD database, including 124,117 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 0.71 ( 38432 hom., cov: 32)
Exomes 𝑓: 0.76 ( 85685 hom. )
Consequence
CHRNB2
NM_000748.3 3_prime_UTR
NM_000748.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.54
Genes affected
CHRNB2 (HGNC:1962): (cholinergic receptor nicotinic beta 2 subunit) Neuronal acetylcholine receptors are homo- or heteropentameric complexes composed of homologous alpha and beta subunits. They belong to a superfamily of ligand-gated ion channels which allow the flow of sodium and potassium across the plasma membrane in response to ligands such as acetylcholine and nicotine. This gene encodes one of several beta subunits. Mutations in this gene are associated with autosomal dominant nocturnal frontal lobe epilepsy. [provided by RefSeq, Jul 2008]
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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=-0.9).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRNB2 | NM_000748.3 | c.*313T>C | 3_prime_UTR_variant | 6/6 | ENST00000368476.4 | ||
CHRNB2 | XM_017000180.3 | c.*313T>C | 3_prime_UTR_variant | 3/3 | |||
CHRNB2 | XR_001736952.3 | n.2089T>C | non_coding_transcript_exon_variant | 6/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNB2 | ENST00000368476.4 | c.*313T>C | 3_prime_UTR_variant | 6/6 | 1 | NM_000748.3 | P4 | ||
CHRNB2 | ENST00000637900.1 | c.*313T>C | 3_prime_UTR_variant | 6/6 | 5 | A1 | |||
CHRNB2 | ENST00000636034.1 | c.1505+317T>C | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.706 AC: 107302AN: 151968Hom.: 38418 Cov.: 32
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GnomAD4 exome AF: 0.764 AC: 223601AN: 292728Hom.: 85685 Cov.: 2 AF XY: 0.769 AC XY: 120335AN XY: 156584
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GnomAD4 genome ? AF: 0.706 AC: 107353AN: 152086Hom.: 38432 Cov.: 32 AF XY: 0.707 AC XY: 52564AN XY: 74372
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ClinVar
Not reported inComputational scores
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Name
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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