rs2067481
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001375978.1(CHRM3):c.193G>A(p.Val65Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0156 in 1,614,116 control chromosomes in the GnomAD database, including 287 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001375978.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRM3 | NM_001375978.1 | c.193G>A | p.Val65Ile | missense_variant | 7/7 | ENST00000676153.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRM3 | ENST00000676153.1 | c.193G>A | p.Val65Ile | missense_variant | 7/7 | NM_001375978.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0135 AC: 2054AN: 152112Hom.: 28 Cov.: 32
GnomAD3 exomes AF: 0.0174 AC: 4386AN: 251400Hom.: 62 AF XY: 0.0197 AC XY: 2683AN XY: 135870
GnomAD4 exome AF: 0.0158 AC: 23099AN: 1461886Hom.: 259 Cov.: 31 AF XY: 0.0168 AC XY: 12200AN XY: 727242
GnomAD4 genome ? AF: 0.0135 AC: 2055AN: 152230Hom.: 28 Cov.: 32 AF XY: 0.0148 AC XY: 1103AN XY: 74440
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2024 | CHRM3: BP4, BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at