7-136868746-GCACACACACACACACA-GCACACACACACACACACACA

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001006630.2(CHRM2):​c.-504_-501dupCACA variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0010 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

CHRM2
NM_001006630.2 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.214
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CHRM2NM_001006630.2 linkc.-504_-501dupCACA 5_prime_UTR_variant Exon 1 of 4 ENST00000680005.1 NP_001006631.1 P08172A4D1Q0Q6SL56Q86SJ1
CHRM2NM_001006627.3 linkc.-426_-423dupCACA 5_prime_UTR_variant Exon 1 of 3 NP_001006628.1 P08172A4D1Q0Q6SL56Q86SJ1
CHRM2NM_001378972.1 linkc.-616_-613dupCACA 5_prime_UTR_variant Exon 1 of 5 NP_001365901.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CHRM2ENST00000680005 linkc.-504_-501dupCACA 5_prime_UTR_variant Exon 1 of 4 NM_001006630.2 ENSP00000505686.1 P08172

Frequencies

GnomAD3 genomes
AF:
0.000998
AC:
149
AN:
149278
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00143
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00433
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000202
Gnomad SAS
AF:
0.00107
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000253
Gnomad OTH
AF:
0.00146
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
196
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
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:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00102
AC:
152
AN:
149384
Hom.:
0
Cov.:
0
AF XY:
0.00121
AC XY:
88
AN XY:
72808
show subpopulations
Gnomad4 AFR
AF:
0.00149
Gnomad4 AMR
AF:
0.00432
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000203
Gnomad4 SAS
AF:
0.00107
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000253
Gnomad4 OTH
AF:
0.00145
Bravo
AF:
0.00122

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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.

Other links and lift over

dbSNP: rs35916399; hg19: chr7-136553493; API