chr4-41257096-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_004181.5(UCHL1):c.34-19C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00239 in 1,613,794 control chromosomes in the GnomAD database, including 73 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.011 ( 36 hom., cov: 33)
Exomes 𝑓: 0.0015 ( 37 hom. )
Consequence
UCHL1
NM_004181.5 intron
NM_004181.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.641
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 -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
?
Variant 4-41257096-C-T is Benign according to our data. Variant chr4-41257096-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1316120.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0114 (1742/152330) while in subpopulation AFR AF= 0.0382 (1588/41584). AF 95% confidence interval is 0.0366. There are 36 homozygotes in gnomad4. There are 807 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1735 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UCHL1 | NM_004181.5 | c.34-19C>T | intron_variant | ENST00000284440.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UCHL1 | ENST00000284440.9 | c.34-19C>T | intron_variant | 1 | NM_004181.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0114 AC: 1735AN: 152212Hom.: 36 Cov.: 33
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GnomAD3 exomes AF: 0.00329 AC: 828AN: 251314Hom.: 12 AF XY: 0.00255 AC XY: 346AN XY: 135906
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GnomAD4 exome AF: 0.00145 AC: 2120AN: 1461464Hom.: 37 Cov.: 32 AF XY: 0.00137 AC XY: 995AN XY: 727052
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 16, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at