rs4475425

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001006630.2(CHRM2):​c.-125+21034G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 152,094 control chromosomes in the GnomAD database, including 7,648 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 0.30 ( 7648 hom., cov: 33)

Consequence

CHRM2
NM_001006630.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.470
Variant links:
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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CHRM2NM_001006630.2 linkc.-125+21034G>A intron_variant Intron 2 of 3 ENST00000680005.1 NP_001006631.1 P08172A4D1Q0Q6SL56Q86SJ1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CHRM2ENST00000680005.1 linkc.-125+21034G>A intron_variant Intron 2 of 3 NM_001006630.2 ENSP00000505686.1 P08172

Frequencies

GnomAD3 genomes
AF:
0.303
AC:
46122
AN:
151976
Hom.:
7634
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.416
Gnomad AMI
AF:
0.274
Gnomad AMR
AF:
0.226
Gnomad ASJ
AF:
0.284
Gnomad EAS
AF:
0.414
Gnomad SAS
AF:
0.342
Gnomad FIN
AF:
0.301
Gnomad MID
AF:
0.231
Gnomad NFE
AF:
0.244
Gnomad OTH
AF:
0.269
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.304
AC:
46176
AN:
152094
Hom.:
7648
Cov.:
33
AF XY:
0.307
AC XY:
22837
AN XY:
74334
show subpopulations
Gnomad4 AFR
AF:
0.416
Gnomad4 AMR
AF:
0.226
Gnomad4 ASJ
AF:
0.284
Gnomad4 EAS
AF:
0.414
Gnomad4 SAS
AF:
0.343
Gnomad4 FIN
AF:
0.301
Gnomad4 NFE
AF:
0.244
Gnomad4 OTH
AF:
0.277
Alfa
AF:
0.254
Hom.:
6730
Bravo
AF:
0.300
Asia WGS
AF:
0.393
AC:
1364
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.71
CADD
Benign
7.3
DANN
Benign
0.46

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs4475425; hg19: chr7-136575199; COSMIC: COSV57768492; API