2-218824242-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_017431.4(PRKAG3):c.1333G>A(p.Asp445Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000743 in 1,614,012 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 (★).
Frequency
Consequence
NM_017431.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRKAG3 | ENST00000439262.7 | c.1333G>A | p.Asp445Asn | missense_variant | Exon 12 of 14 | 1 | ENSP00000397133.3 | |||
PRKAG3 | ENST00000529249.5 | c.1333G>A | p.Asp445Asn | missense_variant | Exon 12 of 13 | 1 | ENSP00000436068.1 | |||
PRKAG3 | ENST00000470307.6 | n.*225G>A | downstream_gene_variant | 5 | ENSP00000419272.2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152132Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251170Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135758
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461880Hom.: 0 Cov.: 33 AF XY: 0.00000688 AC XY: 5AN XY: 727242
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152132Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74296
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1333G>A (p.D445N) alteration is located in exon 12 (coding exon 12) of the PRKAG3 gene. This alteration results from a G to A substitution at nucleotide position 1333, causing the aspartic acid (D) at amino acid position 445 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at