rs10517002

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004181.5(UCHL1):​c.459+609C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 151,786 control chromosomes in the GnomAD database, including 26,708 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.59 ( 26708 hom., cov: 31)

Consequence

UCHL1
NM_004181.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.104
Variant links:
Genes affected
UCHL1 (HGNC:12513): (ubiquitin C-terminal hydrolase L1) The protein encoded by this gene belongs to the peptidase C12 family. This enzyme is a thiol protease that hydrolyzes a peptide bond at the C-terminal glycine of ubiquitin. This gene is specifically expressed in the neurons and in cells of the diffuse neuroendocrine system. Mutations in this gene may be associated with Parkinson disease.[provided by RefSeq, Sep 2009]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
UCHL1NM_004181.5 linkuse as main transcriptc.459+609C>A intron_variant ENST00000284440.9 NP_004172.2 P09936V9HW74

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
UCHL1ENST00000284440.9 linkuse as main transcriptc.459+609C>A intron_variant 1 NM_004181.5 ENSP00000284440.4 P09936

Frequencies

GnomAD3 genomes
AF:
0.591
AC:
89637
AN:
151668
Hom.:
26665
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.550
Gnomad AMI
AF:
0.780
Gnomad AMR
AF:
0.626
Gnomad ASJ
AF:
0.603
Gnomad EAS
AF:
0.790
Gnomad SAS
AF:
0.512
Gnomad FIN
AF:
0.576
Gnomad MID
AF:
0.592
Gnomad NFE
AF:
0.597
Gnomad OTH
AF:
0.603
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.591
AC:
89724
AN:
151786
Hom.:
26708
Cov.:
31
AF XY:
0.590
AC XY:
43778
AN XY:
74140
show subpopulations
Gnomad4 AFR
AF:
0.550
Gnomad4 AMR
AF:
0.626
Gnomad4 ASJ
AF:
0.603
Gnomad4 EAS
AF:
0.790
Gnomad4 SAS
AF:
0.513
Gnomad4 FIN
AF:
0.576
Gnomad4 NFE
AF:
0.598
Gnomad4 OTH
AF:
0.603
Alfa
AF:
0.531
Hom.:
2428
Bravo
AF:
0.600
Asia WGS
AF:
0.630
AC:
2191
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.40
DANN
Benign
0.26

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10517002; hg19: chr4-41264549; API