rs201165506
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001006630.2(CHRM2):c.1030G>A(p.Val344Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,612,994 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V344G) has been classified as Uncertain significance.
Frequency
Consequence
NM_001006630.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRM2 | NM_001006630.2 | c.1030G>A | p.Val344Met | missense_variant | 4/4 | ENST00000680005.1 | |
LOC349160 | NR_046103.1 | n.341+16899C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRM2 | ENST00000680005.1 | c.1030G>A | p.Val344Met | missense_variant | 4/4 | NM_001006630.2 | P1 | ||
ENST00000586239.5 | n.273+16899C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151880Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000400 AC: 10AN: 250176Hom.: 0 AF XY: 0.0000592 AC XY: 8AN XY: 135180
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461114Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 726886
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151880Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74154
ClinVar
Submissions by phenotype
Dilated Cardiomyopathy, Dominant Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Apr 29, 2023 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant  is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 478111). This variant has not been reported in the literature in individuals affected with CHRM2-related conditions. This variant is present in population databases (rs201165506, gnomAD 0.006%). This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 344 of the CHRM2 protein (p.Val344Met). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at