rs193077277
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP2BP4_StrongBP6_Very_StrongBS2
The NM_018206.6(VPS35):c.151G>A(p.Gly51Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00023 in 1,613,488 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_018206.6 missense
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 |
---|---|---|---|---|---|---|---|
VPS35 | NM_018206.6 | c.151G>A | p.Gly51Ser | missense_variant | 3/17 | ENST00000299138.12 | |
VPS35 | XM_011523227.4 | c.64G>A | p.Gly22Ser | missense_variant | 3/17 | ||
VPS35 | XM_005256045.4 | c.-22-607G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VPS35 | ENST00000299138.12 | c.151G>A | p.Gly51Ser | missense_variant | 3/17 | 1 | NM_018206.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000302 AC: 46AN: 152094Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000454 AC: 114AN: 251040Hom.: 0 AF XY: 0.000427 AC XY: 58AN XY: 135674
GnomAD4 exome AF: 0.000222 AC: 325AN: 1461276Hom.: 1 Cov.: 30 AF XY: 0.000226 AC XY: 164AN XY: 726954
GnomAD4 genome ? AF: 0.000302 AC: 46AN: 152212Hom.: 1 Cov.: 32 AF XY: 0.000390 AC XY: 29AN XY: 74430
ClinVar
Submissions by phenotype
Parkinson disease 17 Benign:1Other:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 19, 2023 | - - |
not provided, no classification provided | literature only | GeneReviews | - | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 28, 2020 | See Variant Classification Assertion Criteria. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at