7-136986811-G-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001006630.2(CHRM2):c.-124-5376G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 151,988 control chromosomes in the GnomAD database, including 29,079 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 0.61 ( 29079 hom., cov: 32)
Consequence
CHRM2
NM_001006630.2 intron
NM_001006630.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.486
Publications
3 publications found
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]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.607 AC: 92232AN: 151868Hom.: 29059 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
92232
AN:
151868
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.607 AC: 92278AN: 151988Hom.: 29079 Cov.: 32 AF XY: 0.611 AC XY: 45410AN XY: 74284 show subpopulations
GnomAD4 genome
AF:
AC:
92278
AN:
151988
Hom.:
Cov.:
32
AF XY:
AC XY:
45410
AN XY:
74284
show subpopulations
African (AFR)
AF:
AC:
20186
AN:
41436
American (AMR)
AF:
AC:
8070
AN:
15256
Ashkenazi Jewish (ASJ)
AF:
AC:
2510
AN:
3472
East Asian (EAS)
AF:
AC:
1862
AN:
5158
South Asian (SAS)
AF:
AC:
2656
AN:
4816
European-Finnish (FIN)
AF:
AC:
8262
AN:
10562
Middle Eastern (MID)
AF:
AC:
198
AN:
294
European-Non Finnish (NFE)
AF:
AC:
46657
AN:
67970
Other (OTH)
AF:
AC:
1328
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1750
3501
5251
7002
8752
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
758
1516
2274
3032
3790
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1668
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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