rs517078
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_012125.4(CHRM5):c.-408+15926G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 151,934 control chromosomes in the GnomAD database, including 20,705 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 0.47 ( 20705 hom., cov: 31)
Consequence
CHRM5
NM_012125.4 intron
NM_012125.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.468
Genes affected
CHRM5 (HGNC:1954): (cholinergic receptor muscarinic 5) 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, stimulation of this receptor is known to increase cyclic AMP levels. [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=-0.8).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRM5 | NM_012125.4 | c.-408+15926G>A | intron_variant | ENST00000383263.7 | |||
AVEN | NM_020371.3 | c.445+17956C>T | intron_variant | ENST00000306730.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AVEN | ENST00000306730.8 | c.445+17956C>T | intron_variant | 1 | NM_020371.3 | P1 | |||
CHRM5 | ENST00000383263.7 | c.-408+15926G>A | intron_variant | 2 | NM_012125.4 | P1 | |||
CHRM5 | ENST00000560035.1 | c.-76+15926G>A | intron_variant | 4 | |||||
AVEN | ENST00000675287.1 | n.1815+17956C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.475 AC: 72146AN: 151816Hom.: 20697 Cov.: 31
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?
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.475 AC: 72156AN: 151934Hom.: 20705 Cov.: 31 AF XY: 0.473 AC XY: 35139AN XY: 74254
GnomAD4 genome
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31
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35139
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74254
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1774
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3476
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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