rs13247260

Variant names:

• chr7-136868516-C-A
• rs13247260
• ENST00000439694.6:n.656-82625G>T

Your query was ambiguous. Multiple possible variants found:

• chr7-136868516-C-A
• chr7-136868516-C-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000439694.6(ENSG00000234352):​n.656-82625G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 151,872 control chromosomes in the GnomAD database, including 13,019 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 0.41 (13019 hom., cov: 30)
• Consequence: ENSG00000234352 ENST00000439694.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.366
• Publications: 3 publications found

Genes affected

ENSG00000234352 (HGNC:):

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]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHRM2	NM_001006630.2	c.-759C>A		upstream_gene_variant		ENST00000680005.1	NP_001006631.1
CHRM2	NM_001006627.3	c.-681C>A		upstream_gene_variant			NP_001006628.1
CHRM2	NM_001378972.1	c.-871C>A		upstream_gene_variant			NP_001365901.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHRM2	ENST00000680005.1	c.-759C>A		upstream_gene_variant			NM_001006630.2	ENSP00000505686.1

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61799 AN: 151754 Hom.: 12994 Cov.: 30

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.407 AC: 61862 AN: 151872 Hom.: 13019 Cov.: 30 AF XY: 0.397 AC XY: 29441 AN XY: 74238

African (AFR) AF: 0.454 AC: 18784 AN: 41392

American (AMR) AF: 0.359 AC: 5472 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1380 AN: 3472

East Asian (EAS) AF: 0.124 AC: 641 AN: 5150

South Asian (SAS) AF: 0.278 AC: 1337 AN: 4818

European-Finnish (FIN) AF: 0.331 AC: 3486 AN: 10532

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29314 AN: 67942

Other (OTH) AF: 0.413 AC: 867 AN: 2100

Alfa AF: 0.346 Hom.: 1660

Bravo AF: 0.412

Asia WGS AF: 0.226 AC: 789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	13
DANN	Benign	0.85
PhyloP100		0.37
PromoterAI		0.015	Neutral

Splicing

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

Other links and lift over

dbSNP: rs13247260; hg19: chr7-136553263;