chr7-136950783-C-CTGTTGT

Position:

• chr7-136950783-C-CTGTTGT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001006630.2(CHRM2):​c.-124-41363_-124-41358dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.092 (724 hom., cov: 16)
• Consequence: CHRM2 NM_001006630.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.190

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 7-136950783-C-CTGTTGT is Benign according to our data. Variant chr7-136950783-C-CTGTTGT is described in ClinVar as [Benign]. Clinvar id is 1240542.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHRM2	NM_001006630.2	c.-124-41363_-124-41358dup		intron_variant		ENST00000680005.1
LOC349160	NR_046103.1	n.342-48783_342-48782insACAACA		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHRM2	ENST00000680005.1	c.-124-41363_-124-41358dup		intron_variant			NM_001006630.2	P1
	ENST00000586239.5	n.273+82010_273+82011insACAACA		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0925 AC: 13811 AN: 149314 Hom.: 724 Cov.: 16

Gnomad AFR AF: 0.0468

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.0876

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0737

Gnomad MID AF: 0.0994

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.0877

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

GnomAD4 genome AF: 0.0925 AC: 13820 AN: 149422 Hom.: 724 Cov.: 16 AF XY: 0.0899 AC XY: 6539 AN XY: 72774

Gnomad4 AFR AF: 0.0468

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.0865

Gnomad4 EAS AF: 0.0874

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0737

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.0868

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Apr 27, 2020

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs200954535; hg19: chr7-136635530;