rs17411561

Variant summary

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

The NM_001006630.2(CHRM2):​c.-125+47204T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 150,862 control chromosomes in the GnomAD database, including 4,866 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 0.22 ( 4866 hom., cov: 31)

Consequence

CHRM2
NM_001006630.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.875
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]

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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=-0.87).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CHRM2NM_001006630.2 linkuse as main transcriptc.-125+47204T>C intron_variant ENST00000680005.1
LOC349160NR_046103.1 linkuse as main transcriptn.342-14621A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CHRM2ENST00000680005.1 linkuse as main transcriptc.-125+47204T>C intron_variant NM_001006630.2 P1
ENST00000586239.5 linkuse as main transcriptn.273+116172A>G intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.223
AC:
33564
AN:
150754
Hom.:
4867
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0615
Gnomad AMI
AF:
0.211
Gnomad AMR
AF:
0.228
Gnomad ASJ
AF:
0.290
Gnomad EAS
AF:
0.0395
Gnomad SAS
AF:
0.130
Gnomad FIN
AF:
0.304
Gnomad MID
AF:
0.297
Gnomad NFE
AF:
0.323
Gnomad OTH
AF:
0.259
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.222
AC:
33549
AN:
150862
Hom.:
4866
Cov.:
31
AF XY:
0.220
AC XY:
16185
AN XY:
73702
show subpopulations
Gnomad4 AFR
AF:
0.0613
Gnomad4 AMR
AF:
0.228
Gnomad4 ASJ
AF:
0.290
Gnomad4 EAS
AF:
0.0390
Gnomad4 SAS
AF:
0.130
Gnomad4 FIN
AF:
0.304
Gnomad4 NFE
AF:
0.323
Gnomad4 OTH
AF:
0.256
Alfa
AF:
0.268
Hom.:
786
Bravo
AF:
0.209
Asia WGS
AF:
0.0940
AC:
323
AN:
3438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
5.8
DANN
Benign
0.35

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: rs17411561; hg19: chr7-136601369; API