chr7-136950783-C-CTGT
Variant summary
Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_001006630.2(CHRM2):c.-124-41360_-124-41358dupGTT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.17 ( 2426 hom., cov: 16)
Consequence
CHRM2
NM_001006630.2 intron
NM_001006630.2 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.190
Publications
0 publications found
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 was made for transcript
Our verdict: Benign. The variant received -10 ACMG points.
BP6
Variant 7-136950783-C-CTGT is Benign according to our data. Variant chr7-136950783-C-CTGT is described in ClinVar as Benign. ClinVar VariationId is 1178961.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001006630.2. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CHRM2 | MANE Select | c.-124-41360_-124-41358dupGTT | intron | N/A | NP_001006631.1 | P08172 | |||
| CHRM2 | c.-124-41360_-124-41358dupGTT | intron | N/A | NP_000730.1 | P08172 | ||||
| CHRM2 | c.-202-176_-202-174dupGTT | intron | N/A | NP_001006627.1 | A4D1Q0 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CHRM2 | MANE Select | c.-124-41404_-124-41403insTGT | intron | N/A | ENSP00000505686.1 | P08172 | |||
| CHRM2 | TSL:1 | c.-46-64037_-46-64036insTGT | intron | N/A | ENSP00000319984.5 | P08172 | |||
| CHRM2 | TSL:1 | c.-202-220_-202-219insTGT | intron | N/A | ENSP00000384401.1 | P08172 |
Frequencies
GnomAD3 genomes 0.166 AC: 24786AN: 149012Hom.: 2421 Cov.: 16 show subpopulations
GnomAD3 genomes
AF:
AC:
24786
AN:
149012
Hom.:
Cov.:
16
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.166 AC: 24801AN: 149118Hom.: 2426 Cov.: 16 AF XY: 0.170 AC XY: 12327AN XY: 72610 show subpopulations
GnomAD4 genome
AF:
AC:
24801
AN:
149118
Hom.:
Cov.:
16
AF XY:
AC XY:
12327
AN XY:
72610
show subpopulations
African (AFR)
AF:
AC:
5108
AN:
40748
American (AMR)
AF:
AC:
4132
AN:
14778
Ashkenazi Jewish (ASJ)
AF:
AC:
460
AN:
3452
East Asian (EAS)
AF:
AC:
1740
AN:
4860
South Asian (SAS)
AF:
AC:
1236
AN:
4570
European-Finnish (FIN)
AF:
AC:
1538
AN:
10162
Middle Eastern (MID)
AF:
AC:
34
AN:
288
European-Non Finnish (NFE)
AF:
AC:
10085
AN:
67280
Other (OTH)
AF:
AC:
355
AN:
2076
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.441
Heterozygous variant carriers
0
818
1636
2454
3272
4090
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
278
556
834
1112
1390
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
ClinVar
ClinVar submissions
View on ClinVar Significance:Benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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