rs661968
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_012125.4(CHRM5):c.-690C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 152,034 control chromosomes in the GnomAD database, including 54,276 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 0.80 ( 54276 hom., cov: 31)
Exomes 𝑓: 1.0 ( 5 hom. )
Failed GnomAD Quality Control
Consequence
CHRM5
NM_012125.4 5_prime_UTR
NM_012125.4 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.98
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 -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.23).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRM5 | NM_012125.4 | c.-690C>T | 5_prime_UTR_variant | 1/3 | ENST00000383263.7 | ||
AVEN | NM_020371.3 | c.445+34164G>A | intron_variant | ENST00000306730.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRM5 | ENST00000383263.7 | c.-690C>T | 5_prime_UTR_variant | 1/3 | 2 | NM_012125.4 | P1 | ||
AVEN | ENST00000306730.8 | c.445+34164G>A | intron_variant | 1 | NM_020371.3 | P1 | |||
CHRM5 | ENST00000560035.1 | c.-358C>T | 5_prime_UTR_variant | 1/2 | 4 | ||||
AVEN | ENST00000675287.1 | n.1815+34164G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.805 AC: 122293AN: 151916Hom.: 54275 Cov.: 31
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 1.00 AC: 10AN: 10Hom.: 5 Cov.: 0 AF XY: 1.00 AC XY: 6AN XY: 6
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome ? AF: 0.805 AC: 122326AN: 152034Hom.: 54276 Cov.: 31 AF XY: 0.811 AC XY: 60276AN XY: 74340
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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