chr17-553417-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001128159.3(VPS53):c.1750C>G(p.Arg584Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00000274 in 1,461,800 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. R584R) has been classified as Likely benign.
Frequency
Consequence
NM_001128159.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VPS53 | NM_001128159.3 | c.1750C>G | p.Arg584Gly | missense_variant | 16/22 | ENST00000437048.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VPS53 | ENST00000437048.7 | c.1750C>G | p.Arg584Gly | missense_variant | 16/22 | 1 | NM_001128159.3 | P1 | |
ENST00000574008.1 | n.592G>C | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 30
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251396Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135886
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461800Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727212
GnomAD4 genome ? Cov.: 30
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at