rs60038135
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_000747.3(CHRNB1):c.198+36G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000144 in 1,602,716 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000014 ( 0 hom. )
Consequence
CHRNB1
NM_000747.3 intron
NM_000747.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.04
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 Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRNB1 | NM_000747.3 | c.198+36G>A | intron_variant | ENST00000306071.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNB1 | ENST00000306071.7 | c.198+36G>A | intron_variant | 1 | NM_000747.3 | P1 | |||
CHRNB1 | ENST00000570557.5 | c.71+36G>A | intron_variant | 5 | |||||
CHRNB1 | ENST00000572857.5 | c.198+36G>A | intron_variant | 4 | |||||
CHRNB1 | ENST00000574054.1 | n.254G>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000199 AC: 3AN: 150912Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000271 AC: 6AN: 221490Hom.: 0 AF XY: 0.0000327 AC XY: 4AN XY: 122350
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GnomAD4 exome AF: 0.0000138 AC: 20AN: 1451682Hom.: 0 Cov.: 34 AF XY: 0.0000194 AC XY: 14AN XY: 721822
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GnomAD4 genome ? AF: 0.0000199 AC: 3AN: 151034Hom.: 0 Cov.: 32 AF XY: 0.0000271 AC XY: 2AN XY: 73858
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Not reported inComputational scores
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Benign
CADD
Benign
DANN
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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