rs8191993
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001006630.2(CHRM2):c.*550G>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 0.707 in 167,350 control chromosomes in the GnomAD database, including 42,470 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 0.70 ( 37955 hom., cov: 32)
Exomes 𝑓: 0.76 ( 4515 hom. )
Consequence
CHRM2
NM_001006630.2 3_prime_UTR
NM_001006630.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.497
Genes affected
CHRM2 (HGNC:1951): (cholinergic receptor muscarinic 2) The muscarinic cholinergic receptors belong to a larger family of G protein-coupled receptors. The functional diversity of these receptors is defined by the binding of acetylcholine to these receptors and includes cellular responses such as adenylate cyclase inhibition, phosphoinositide degeneration, and potassium channel mediation. Muscarinic receptors influence many effects of acetylcholine in the central and peripheral nervous system. The muscarinic cholinergic receptor 2 is involved in mediation of bradycardia and a decrease in cardiac contractility. Multiple alternatively spliced transcript variants have been described for this gene. [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=-0.89).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRM2 | NM_001006630.2 | c.*550G>C | 3_prime_UTR_variant | 4/4 | ENST00000680005.1 | ||
LOC349160 | NR_046103.1 | n.341+15978C>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRM2 | ENST00000680005.1 | c.*550G>C | 3_prime_UTR_variant | 4/4 | NM_001006630.2 | P1 | |||
ENST00000586239.5 | n.273+15978C>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.701 AC: 106381AN: 151708Hom.: 37914 Cov.: 32
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GnomAD4 exome AF: 0.763 AC: 11841AN: 15524Hom.: 4515 Cov.: 0 AF XY: 0.763 AC XY: 5644AN XY: 7394
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GnomAD4 genome ? AF: 0.701 AC: 106471AN: 151826Hom.: 37955 Cov.: 32 AF XY: 0.701 AC XY: 51995AN XY: 74184
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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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at