7-136868746-GCACACA-G

Variant summary

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

The NM_001006630.2(CHRM2):c.-506_-501del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 149,490 control chromosomes in the GnomAD database, including 1,137 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.11 (1137 hom., cov: 0)
  • Exomes 𝑓: 0.036 (0 hom.)
• Consequence: CHRM2 NM_001006630.2 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 3.33

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 7-136868746-GCACACA-G is Benign according to our data. Variant chr7-136868746-GCACACA-G is described in ClinVar as [Benign]. Clinvar id is 1270234.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHRM2	NM_001006630.2	c.-506_-501del		5_prime_UTR_variant	1/4	ENST00000680005.1
CHRM2	NM_001006627.3	c.-428_-423del		5_prime_UTR_variant	1/3
CHRM2	NM_001378972.1	c.-618_-613del		5_prime_UTR_variant	1/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHRM2	ENST00000680005.1	c.-506_-501del		5_prime_UTR_variant	1/4		NM_001006630.2	P1
	ENST00000586239.5	n.274-82861_274-82856del		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.107 AC: 15904 AN: 149188 Hom.: 1135 Cov.: 0

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.0727

Gnomad ASJ AF: 0.0920

Gnomad EAS AF: 0.00526

Gnomad SAS AF: 0.0401

Gnomad FIN AF: 0.0430

Gnomad MID AF: 0.0927

Gnomad NFE AF: 0.0830

Gnomad OTH AF: 0.0915

GnomAD4 exome AF: 0.0357 AC: 7 AN: 196 Hom.: 0 AF XY: 0.0305 AC XY: 5 AN XY: 164

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.0345

Gnomad4 OTH exome AF: 0.125

GnomAD4 genome AF: 0.107 AC: 15926 AN: 149294 Hom.: 1137 Cov.: 0 AF XY: 0.102 AC XY: 7456 AN XY: 72756

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.0726

Gnomad4 ASJ AF: 0.0920

Gnomad4 EAS AF: 0.00528

Gnomad4 SAS AF: 0.0408

Gnomad4 FIN AF: 0.0430

Gnomad4 NFE AF: 0.0830

Gnomad4 OTH AF: 0.0906

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

May 29, 2020

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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: rs35916399; hg19: chr7-136553493;