rs2302761
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000747.3(CHRNB1):c.1045-83C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 1,470,170 control chromosomes in the GnomAD database, including 31,738 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.18 ( 2692 hom., cov: 30)
Exomes 𝑓: 0.20 ( 29046 hom. )
Consequence
CHRNB1
NM_000747.3 intron
NM_000747.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.101
Genes affected
CHRNB1 (HGNC:1961): (cholinergic receptor nicotinic beta 1 subunit) The muscle acetylcholine receptor is composed of five subunits: two alpha subunits and one beta, one gamma, and one delta subunit. This gene encodes the beta subunit of the acetylcholine receptor. The acetylcholine receptor changes conformation upon acetylcholine binding leading to the opening of an ion-conducting channel across the plasma membrane. Mutations in this gene are associated with slow-channel congenital myasthenic syndrome. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BP6
?
Variant 17-7455201-C-T is Benign according to our data. Variant chr17-7455201-C-T is described in ClinVar as [Benign]. Clinvar id is 1293280.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRNB1 | NM_000747.3 | c.1045-83C>T | intron_variant | ENST00000306071.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNB1 | ENST00000306071.7 | c.1045-83C>T | intron_variant | 1 | NM_000747.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.182 AC: 27591AN: 151910Hom.: 2697 Cov.: 30
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GnomAD4 exome AF: 0.204 AC: 268521AN: 1318142Hom.: 29046 AF XY: 0.206 AC XY: 136928AN XY: 663372
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GnomAD4 genome ? AF: 0.182 AC: 27595AN: 152028Hom.: 2692 Cov.: 30 AF XY: 0.180 AC XY: 13355AN XY: 74304
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 07, 2018 | - - |
Computational 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