Variant chr7-136950870-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001006630.2(CHRM2):c.-124-41317C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 152,068 control chromosomes in the GnomAD database, including 31,366 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.64 ( 31326 hom., cov: 31)

Exomes 𝑓: 0.58 ( 40 hom. )

Consequence

CHRM2
NM_001006630.2 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.627

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]

CHRM2 links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.02).

BP6

Variant 7-136950870-C-T is Benign according to our data. Variant chr7-136950870-C-T is described in ClinVar as [Benign]. Clinvar id is 1226056.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHRM2	NM_001006630.2 linkuse as main transcript	c.-124-41317C>T		intron_variant		ENST00000680005.1
LOC349160	NR_046103.1 linkuse as main transcript	n.342-48869G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHRM2	ENST00000680005.1 linkuse as main transcript	c.-124-41317C>T		intron_variant			NM_001006630.2	P1
	ENST00000586239.5 linkuse as main transcript	n.273+81924G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.637

AC:

96699

AN:

151706

Hom.:

31292

Cov.:

show subpopulations

Gnomad AFR

AF:

0.681

Gnomad AMI

AF:

0.611

Gnomad AMR

AF:

0.517

Gnomad ASJ

AF:

0.660

Gnomad EAS

AF:

0.445

Gnomad SAS

AF:

0.481

Gnomad FIN

AF:

0.663

Gnomad MID

AF:

0.589

Gnomad NFE

AF:

0.659

Gnomad OTH

AF:

0.634

GnomAD4 exome

AF:

0.583

AC:

141

AN:

242

Hom.:

AF XY:

0.572

AC XY:

111

AN XY:

194

show subpopulations

Gnomad4 AFR exome

AF:

0.750

Gnomad4 AMR exome

AF:

0.500

Gnomad4 ASJ exome

AF:

0.500

Gnomad4 EAS exome

AF:

0.200

Gnomad4 SAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.750

Gnomad4 NFE exome

AF:

0.590

Gnomad4 OTH exome

AF:

0.667

GnomAD4 genome

AF:

0.637

AC:

96781

AN:

151826

Hom.:

31326

Cov.:

AF XY:

0.633

AC XY:

46954

AN XY:

74212

show subpopulations

Gnomad4 AFR

AF:

0.681

Gnomad4 AMR

AF:

0.516

Gnomad4 ASJ

AF:

0.660

Gnomad4 EAS

AF:

0.445

Gnomad4 SAS

AF:

0.481

Gnomad4 FIN

AF:

0.663

Gnomad4 NFE

AF:

0.659

Gnomad4 OTH

AF:

0.638

Alfa

AF:

0.632

Hom.:

5216

Bravo

AF:

0.627

Asia WGS

AF:

0.495

AC:

1720

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 23, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.57

DANN

Benign

0.31

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over