chr2-218823787-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_017431.4(PRKAG3):c.1445C>T(p.Ala482Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00121 in 1,614,120 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts 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_017431.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRKAG3 | NM_017431.4 | c.1445C>T | p.Ala482Val | missense_variant | 13/14 | ENST00000439262.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKAG3 | ENST00000439262.7 | c.1445C>T | p.Ala482Val | missense_variant | 13/14 | 1 | NM_017431.4 | P1 | |
PRKAG3 | ENST00000529249.5 | c.1445C>T | p.Ala482Val | missense_variant | 13/13 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00571 AC: 869AN: 152206Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.00164 AC: 412AN: 251346Hom.: 3 AF XY: 0.00119 AC XY: 161AN XY: 135856
GnomAD4 exome AF: 0.000737 AC: 1077AN: 1461796Hom.: 12 Cov.: 31 AF XY: 0.000660 AC XY: 480AN XY: 727200
GnomAD4 genome ? AF: 0.00574 AC: 874AN: 152324Hom.: 6 Cov.: 32 AF XY: 0.00600 AC XY: 447AN XY: 74490
ClinVar
Submissions by phenotype
PRKAG3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 25, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at