chr7-136967060-T-A
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.-124-25127T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.877 in 151,894 control chromosomes in the GnomAD database, including 58,991 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 0.88 ( 58991 hom., cov: 30)
Consequence
CHRM2
NM_001006630.2 intron
NM_001006630.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.00800
Publications
1 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]
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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=-0.92).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.877 AC: 133181AN: 151776Hom.: 58972 Cov.: 30 show subpopulations
GnomAD3 genomes
AF:
AC:
133181
AN:
151776
Hom.:
Cov.:
30
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: 0.877 AC: 133244AN: 151894Hom.: 58991 Cov.: 30 AF XY: 0.877 AC XY: 65135AN XY: 74248 show subpopulations
GnomAD4 genome
AF:
AC:
133244
AN:
151894
Hom.:
Cov.:
30
AF XY:
AC XY:
65135
AN XY:
74248
show subpopulations
African (AFR)
AF:
AC:
33997
AN:
41454
American (AMR)
AF:
AC:
11442
AN:
15224
Ashkenazi Jewish (ASJ)
AF:
AC:
3379
AN:
3466
East Asian (EAS)
AF:
AC:
3648
AN:
5168
South Asian (SAS)
AF:
AC:
4020
AN:
4820
European-Finnish (FIN)
AF:
AC:
10257
AN:
10598
Middle Eastern (MID)
AF:
AC:
285
AN:
294
European-Non Finnish (NFE)
AF:
AC:
63498
AN:
67850
Other (OTH)
AF:
AC:
1858
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
775
1550
2324
3099
3874
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2738
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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