rs658842

Variant names:

• chr1-239785335-T-A
• rs658842
• NM_001375978.1:c.-146-41917T>A

Your query was ambiguous. Multiple possible variants found:

• chr1-239785335-T-A
• chr1-239785335-T-C
• chr1-239785335-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001375978.1(CHRM3):​c.-146-41917T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 152,120 control chromosomes in the GnomAD database, including 26,631 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 0.57 (26631 hom., cov: 33)
• Consequence: CHRM3 NM_001375978.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.808
• Publications: 0 publications found

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]

CHRM3 Gene-Disease associations (from GenCC):

• prune belly syndrome

  Inheritance: AD, AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001375978.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHRM3	NM_001375978.1	MANE Select	c.-146-41917T>A		intron	N/A	NP_001362907.1	P20309
	CHRM3	NM_000740.4		c.-146-41917T>A		intron	N/A	NP_000731.1	P20309
	CHRM3	NM_001347716.2		c.-375-41518T>A		intron	N/A	NP_001334645.1	P20309

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHRM3	ENST00000676153.1	MANE Select	c.-146-41917T>A		intron	N/A	ENSP00000502667.1	P20309
	CHRM3	ENST00000255380.8	TSL:1	c.-146-41917T>A		intron	N/A	ENSP00000255380.4	P20309
	CHRM3	ENST00000615928.5	TSL:5	c.-146-41917T>A		intron	N/A	ENSP00000482377.1	P20309

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86829 AN: 152002 Hom.: 26590 Cov.: 33

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.534

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.571 AC: 86929 AN: 152120 Hom.: 26631 Cov.: 33 AF XY: 0.565 AC XY: 42045 AN XY: 74368

African (AFR) AF: 0.798 AC: 33140 AN: 41506

American (AMR) AF: 0.530 AC: 8091 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1736 AN: 3470

East Asian (EAS) AF: 0.607 AC: 3141 AN: 5172

South Asian (SAS) AF: 0.533 AC: 2567 AN: 4820

European-Finnish (FIN) AF: 0.378 AC: 3999 AN: 10574

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.478 AC: 32500 AN: 67990

Other (OTH) AF: 0.535 AC: 1127 AN: 2108

Alfa AF: 0.530 Hom.: 2790

Bravo AF: 0.593

Asia WGS AF: 0.576 AC: 2002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.1
DANN	Benign	0.79
PhyloP100		0.81
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs658842; hg19: chr1-239948635;