7-136868746-GCACACA-G
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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
NM_001006630.2 5_prime_UTR
Scores
Not classified
Clinical Significance
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]
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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 |
---|---|---|---|---|---|---|---|---|
CHRM2 | NM_001006630.2 | c.-506_-501del | 5_prime_UTR_variant | 1/4 | ENST00000680005.1 | NP_001006631.1 | ||
CHRM2 | NM_001006627.3 | c.-428_-423del | 5_prime_UTR_variant | 1/3 | NP_001006628.1 | |||
CHRM2 | NM_001378972.1 | c.-618_-613del | 5_prime_UTR_variant | 1/5 | NP_001365901.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHRM2 | ENST00000680005.1 | c.-506_-501del | 5_prime_UTR_variant | 1/4 | NM_001006630.2 | ENSP00000505686 | P1 | |||
ENST00000586239.5 | n.274-82861_274-82856del | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.107 AC: 15904AN: 149188Hom.: 1135 Cov.: 0
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GnomAD4 exome AF: 0.0357 AC: 7AN: 196Hom.: 0 AF XY: 0.0305 AC XY: 5AN XY: 164
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GnomAD4 genome AF: 0.107 AC: 15926AN: 149294Hom.: 1137 Cov.: 0 AF XY: 0.102 AC XY: 7456AN XY: 72756
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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 submitter | clinical testing | GeneDx | May 29, 2020 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at