7-136869276-G-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001006630.2(CHRM2):c.-267G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00653 in 152,590 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0065 ( 7 hom., cov: 32)
Exomes 𝑓: 0.0069 ( 0 hom. )
Consequence
CHRM2
NM_001006630.2 5_prime_UTR
NM_001006630.2 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.610
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.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
Variant 7-136869276-G-A is Benign according to our data. Variant chr7-136869276-G-A is described in ClinVar as [Benign]. Clinvar id is 384721.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 7 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHRM2 | NM_001006630.2 | c.-267G>A | 5_prime_UTR_variant | 2/4 | ENST00000680005.1 | NP_001006631.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHRM2 | ENST00000680005.1 | c.-267G>A | 5_prime_UTR_variant | 2/4 | NM_001006630.2 | ENSP00000505686 | P1 | |||
ENST00000586239.5 | n.274-83385C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00654 AC: 996AN: 152184Hom.: 7 Cov.: 32
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GnomAD4 exome AF: 0.00694 AC: 2AN: 288Hom.: 0 Cov.: 0 AF XY: 0.00952 AC XY: 2AN XY: 210
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GnomAD4 genome AF: 0.00653 AC: 995AN: 152302Hom.: 7 Cov.: 32 AF XY: 0.00606 AC XY: 451AN XY: 74468
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 26, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at