rs2067482
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000741.5(CHRM4):c.1341C>T(p.Thr447=) variant causes a synonymous change. The variant allele was found at a frequency of 0.155 in 1,613,938 control chromosomes in the GnomAD database, including 20,553 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 0.14 ( 1551 hom., cov: 33)
Exomes 𝑓: 0.16 ( 19002 hom. )
Consequence
CHRM4
NM_000741.5 synonymous
NM_000741.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.74
Genes affected
CHRM4 (HGNC:1953): (cholinergic receptor muscarinic 4) 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 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 clinical implications of this receptor are unknown; however, mouse studies link its function to adenylyl cyclase inhibition. [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=-0.48).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHRM4 | NM_000741.5 | c.1341C>T | p.Thr447= | synonymous_variant | 2/2 | ENST00000682254.1 | NP_000732.2 | |
CHRM4 | NM_001366692.2 | c.1341C>T | p.Thr447= | synonymous_variant | 2/2 | NP_001353621.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHRM4 | ENST00000682254.1 | c.1341C>T | p.Thr447= | synonymous_variant | 2/2 | NM_000741.5 | ENSP00000507561 | P1 | ||
CHRM4 | ENST00000433765.3 | c.1341C>T | p.Thr447= | synonymous_variant | 1/1 | ENSP00000409378 | P1 |
Frequencies
GnomAD3 genomes AF: 0.139 AC: 21189AN: 152144Hom.: 1554 Cov.: 33
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GnomAD3 exomes AF: 0.134 AC: 33632AN: 250384Hom.: 2521 AF XY: 0.139 AC XY: 18787AN XY: 135578
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GnomAD4 exome AF: 0.157 AC: 229734AN: 1461676Hom.: 19002 Cov.: 33 AF XY: 0.157 AC XY: 114510AN XY: 727110
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GnomAD4 genome AF: 0.139 AC: 21190AN: 152262Hom.: 1551 Cov.: 33 AF XY: 0.137 AC XY: 10198AN XY: 74454
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Not reported inComputational 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