7-136868746-GCACACA-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

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

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.33
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 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 Protein UniProt
CHRM2NM_001006630.2 linkuse as main transcriptc.-506_-501del 5_prime_UTR_variant 1/4 ENST00000680005.1 NP_001006631.1
CHRM2NM_001006627.3 linkuse as main transcriptc.-428_-423del 5_prime_UTR_variant 1/3 NP_001006628.1
CHRM2NM_001378972.1 linkuse as main transcriptc.-618_-613del 5_prime_UTR_variant 1/5 NP_001365901.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CHRM2ENST00000680005.1 linkuse as main transcriptc.-506_-501del 5_prime_UTR_variant 1/4 NM_001006630.2 ENSP00000505686 P1
ENST00000586239.5 linkuse as main transcriptn.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
show subpopulations
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
show subpopulations
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
show subpopulations
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
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxMay 29, 2020- -

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