rs5030732
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004181.5(UCHL1):c.53C>A(p.Ser18Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 1,550,242 control chromosomes in the GnomAD database, including 33,472 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_004181.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UCHL1 | NM_004181.5 | c.53C>A | p.Ser18Tyr | missense_variant | 3/9 | ENST00000284440.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UCHL1 | ENST00000284440.9 | c.53C>A | p.Ser18Tyr | missense_variant | 3/9 | 1 | NM_004181.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.166 AC: 25316AN: 152054Hom.: 2979 Cov.: 33
GnomAD3 exomes AF: 0.242 AC: 37510AN: 154918Hom.: 5650 AF XY: 0.242 AC XY: 20429AN XY: 84480
GnomAD4 exome AF: 0.195 AC: 272507AN: 1398072Hom.: 30487 Cov.: 33 AF XY: 0.198 AC XY: 137028AN XY: 691480
GnomAD4 genome ? AF: 0.167 AC: 25340AN: 152170Hom.: 2985 Cov.: 33 AF XY: 0.171 AC XY: 12709AN XY: 74404
ClinVar
Submissions by phenotype
Parkinson disease 5, autosomal dominant, susceptibility to Uncertain:1Benign:4
Benign, criteria provided, single submitter | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | Sep 21, 2015 | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | Feb 07, 2015 | - - |
Uncertain significance, no assertion criteria provided | literature only | OMIM | Jun 01, 2011 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 20, 2021 | This variant is associated with the following publications: (PMID: 12705903, 21700325, 19864305, 19683447, 21251915, 21298373, 18411255, 22076440, 21268678, 17287139, 25370916, 10563640, 33028204, 12408865) - |
Early-onset progressive neurodegeneration-blindness-ataxia-spasticity syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at