chr17-519231-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS1
The NM_001128159.3(VPS53):c.2396C>T(p.Ser799Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0002 in 1,548,954 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. S799S) has been classified as Likely benign.
Frequency
Consequence
NM_001128159.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VPS53 | NM_001128159.3 | c.2396C>T | p.Ser799Leu | missense_variant | 22/22 | ENST00000437048.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VPS53 | ENST00000437048.7 | c.2396C>T | p.Ser799Leu | missense_variant | 22/22 | 1 | NM_001128159.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000145 AC: 22AN: 152248Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000545 AC: 83AN: 152330Hom.: 0 AF XY: 0.000717 AC XY: 58AN XY: 80910
GnomAD4 exome AF: 0.000206 AC: 288AN: 1396590Hom.: 2 Cov.: 30 AF XY: 0.000286 AC XY: 197AN XY: 688866
GnomAD4 genome ? AF: 0.000144 AC: 22AN: 152364Hom.: 0 Cov.: 32 AF XY: 0.000174 AC XY: 13AN XY: 74508
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
VPS53-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 21, 2022 | This variant is classified as likely 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