rs770029606
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP4
The NM_018206.6(VPS35):c.946C>T(p.Pro316Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000161 in 1,610,730 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_018206.6 missense
Scores
Clinical Significance
Conservation
Publications
- Parkinson diseaseInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
- Parkinson disease 17Inheritance: AD Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, Genomics England PanelApp
- hereditary late onset Parkinson diseaseInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- intellectual disabilityInheritance: AR Classification: LIMITED Submitted by: Ambry Genetics
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ACMG classification
Our verdict: Likely_benign. The variant received -1 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_018206.6. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| VPS35 | TSL:1 MANE Select | c.946C>T | p.Pro316Ser | missense | Exon 9 of 17 | ENSP00000299138.7 | Q96QK1 | ||
| VPS35 | TSL:1 | n.*1616C>T | non_coding_transcript_exon | Exon 9 of 17 | ENSP00000456274.2 | H3BRJ7 | |||
| VPS35 | TSL:1 | n.*1616C>T | 3_prime_UTR | Exon 9 of 17 | ENSP00000456274.2 | H3BRJ7 |
Frequencies
GnomAD3 genomes AF: 0.000106 AC: 16AN: 150728Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000768 AC: 19AN: 247278 AF XY: 0.000105 show subpopulations
GnomAD4 exome AF: 0.000167 AC: 244AN: 1460002Hom.: 0 Cov.: 33 AF XY: 0.000171 AC XY: 124AN XY: 726124 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.000106 AC: 16AN: 150728Hom.: 0 Cov.: 32 AF XY: 0.0000817 AC XY: 6AN XY: 73432 show subpopulations
Age Distribution
ClinVar
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at