rs1554405928
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_ModeratePM2
The NM_018238.4(AGK):c.1142dupG(p.Ser382fs) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,460,918 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
AGK
NM_018238.4 frameshift
NM_018238.4 frameshift
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.36
Genes affected
AGK (HGNC:21869): (acylglycerol kinase) The protein encoded by this gene is a mitochondrial membrane protein involved in lipid and glycerolipid metabolism. The encoded protein is a lipid kinase that catalyzes the formation of phosphatidic and lysophosphatidic acids. Defects in this gene have been associated with mitochondrial DNA depletion syndrome 10. [provided by RefSeq, Feb 2012]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.0993 CDS is truncated, and there are 0 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AGK | NM_018238.4 | c.1142dupG | p.Ser382fs | frameshift_variant | 16/16 | ENST00000649286.2 | NP_060708.1 | |
AGK | XM_011516397.4 | c.1142dupG | p.Ser382fs | frameshift_variant | 16/16 | XP_011514699.1 | ||
AGK | XM_024446835.2 | c.1142dupG | p.Ser382fs | frameshift_variant | 16/16 | XP_024302603.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250720Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135550
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GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460918Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 726786
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GnomAD4 genome Cov.: 32
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32
ClinVar
Not reported inComputational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at