rs7214344
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000747.3(CHRNB1):c.1217+28G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.994 in 1,613,656 control chromosomes in the GnomAD database, including 798,356 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.97 ( 72030 hom., cov: 31)
Exomes 𝑓: 1.0 ( 726326 hom. )
Consequence
CHRNB1
NM_000747.3 intron
NM_000747.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.327
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 -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant 17-7455484-G-A is Benign according to our data. Variant chr17-7455484-G-A is described in ClinVar as [Benign]. Clinvar id is 256772.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRNB1 | NM_000747.3 | c.1217+28G>A | intron_variant | ENST00000306071.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNB1 | ENST00000306071.7 | c.1217+28G>A | intron_variant | 1 | NM_000747.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.972 AC: 147840AN: 152110Hom.: 71985 Cov.: 31
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GnomAD3 exomes AF: 0.992 AC: 249316AN: 251222Hom.: 123791 AF XY: 0.994 AC XY: 135064AN XY: 135838
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GnomAD4 exome AF: 0.997 AC: 1456816AN: 1461428Hom.: 726326 Cov.: 37 AF XY: 0.997 AC XY: 725112AN XY: 727048
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GnomAD4 genome ? AF: 0.972 AC: 147943AN: 152228Hom.: 72030 Cov.: 31 AF XY: 0.972 AC XY: 72386AN XY: 74436
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Congenital myasthenic syndrome 2A Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 22, 2021 | - - |
Congenital myasthenic syndrome 2C Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 22, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 16, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at