1-239903960-G-A

Variant summary

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

The NM_001375978.1(CHRM3):​c.-19-3473G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 152,036 control chromosomes in the GnomAD database, including 27,476 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 0.59 ( 27476 hom., cov: 32)

Consequence

CHRM3
NM_001375978.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.354
Variant links:
Genes affected
CHRM3 (HGNC:1952): (cholinergic receptor muscarinic 3) 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 muscarinic cholinergic receptor 3 controls smooth muscle contraction and its stimulation causes secretion of glandular tissue. Alternative promoter use and alternative splicing results in multiple transcript variants that have different tissue specificities. [provided by RefSeq, Dec 2016]

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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=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CHRM3NM_001375978.1 linkuse as main transcriptc.-19-3473G>A intron_variant ENST00000676153.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CHRM3ENST00000676153.1 linkuse as main transcriptc.-19-3473G>A intron_variant NM_001375978.1 P1

Frequencies

GnomAD3 genomes
AF:
0.595
AC:
90319
AN:
151918
Hom.:
27443
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.705
Gnomad AMI
AF:
0.559
Gnomad AMR
AF:
0.541
Gnomad ASJ
AF:
0.466
Gnomad EAS
AF:
0.479
Gnomad SAS
AF:
0.529
Gnomad FIN
AF:
0.698
Gnomad MID
AF:
0.456
Gnomad NFE
AF:
0.545
Gnomad OTH
AF:
0.564
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.595
AC:
90408
AN:
152036
Hom.:
27476
Cov.:
32
AF XY:
0.597
AC XY:
44368
AN XY:
74312
show subpopulations
Gnomad4 AFR
AF:
0.705
Gnomad4 AMR
AF:
0.541
Gnomad4 ASJ
AF:
0.466
Gnomad4 EAS
AF:
0.479
Gnomad4 SAS
AF:
0.527
Gnomad4 FIN
AF:
0.698
Gnomad4 NFE
AF:
0.545
Gnomad4 OTH
AF:
0.565
Alfa
AF:
0.543
Hom.:
47257
Bravo
AF:
0.588
Asia WGS
AF:
0.515
AC:
1795
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
2.4
DANN
Benign
0.38

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: rs7520974; hg19: chr1-240067260; API