chr17-519230-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 2P and 17B. PM2BP4_StrongBP6_Very_StrongBP7BS1
The NM_001128159.3(VPS53):c.2397G>A(p.Ser799=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000125 in 1,548,810 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 Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. S799S) has been classified as Likely benign.
Frequency
Consequence
NM_001128159.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VPS53 | NM_001128159.3 | c.2397G>A | p.Ser799= | synonymous_variant | 22/22 | ENST00000437048.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VPS53 | ENST00000437048.7 | c.2397G>A | p.Ser799= | synonymous_variant | 22/22 | 1 | NM_001128159.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000657 AC: 100AN: 152236Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000112 AC: 17AN: 152200Hom.: 0 AF XY: 0.0000371 AC XY: 3AN XY: 80874
GnomAD4 exome AF: 0.0000673 AC: 94AN: 1396456Hom.: 0 Cov.: 30 AF XY: 0.0000523 AC XY: 36AN XY: 688808
GnomAD4 genome AF: 0.000656 AC: 100AN: 152354Hom.: 0 Cov.: 32 AF XY: 0.000631 AC XY: 47AN XY: 74496
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 05, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at