rs944947
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_013438.5(UBQLN1):c.332+855A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 139,570 control chromosomes in the GnomAD database, including 3,170 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 0.21 ( 3170 hom., cov: 31)
Consequence
UBQLN1
NM_013438.5 intron
NM_013438.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.56
Genes affected
UBQLN1 (HGNC:12508): (ubiquilin 1) This gene encodes an ubiquitin-like protein (ubiquilin) that shares a high degree of similarity with related products in yeast, rat and frog. Ubiquilins contain an N-terminal ubiquitin-like domain and a C-terminal ubiquitin-associated domain. They physically associate with both proteasomes and ubiquitin ligases, and thus are thought to functionally link the ubiquitination machinery to the proteasome to affect in vivo protein degradation. This ubiquilin has also been shown to modulate accumulation of presenilin proteins, and it is found in lesions associated with Alzheimer's and Parkinson's disease. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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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=-0.98).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UBQLN1 | NM_013438.5 | c.332+855A>G | intron_variant | ENST00000376395.9 | |||
UBQLN1 | NM_053067.3 | c.332+855A>G | intron_variant | ||||
UBQLN1 | XM_005251948.4 | c.332+855A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBQLN1 | ENST00000376395.9 | c.332+855A>G | intron_variant | 1 | NM_013438.5 | P3 | |||
UBQLN1 | ENST00000257468.11 | c.332+855A>G | intron_variant | 1 | A1 | ||||
UBQLN1 | ENST00000533705.5 | n.50+855A>G | intron_variant, non_coding_transcript_variant | 1 | |||||
UBQLN1 | ENST00000529923.1 | c.103-6550A>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.214 AC: 29819AN: 139482Hom.: 3170 Cov.: 31
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GnomAD4 genome ? AF: 0.214 AC: 29829AN: 139570Hom.: 3170 Cov.: 31 AF XY: 0.214 AC XY: 14491AN XY: 67588
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at