rs6845147
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003715.4(USO1):c.1987-194G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 151,898 control chromosomes in the GnomAD database, including 23,440 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 0.53 ( 23440 hom., cov: 31)
Consequence
USO1
NM_003715.4 intron
NM_003715.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.385
Genes affected
USO1 (HGNC:30904): (USO1 vesicle transport factor) The protein encoded by this gene is a peripheral membrane protein which recycles between the cytosol and the Golgi apparatus during interphase. It is regulated by phosphorylation: dephosphorylated protein associates with the Golgi membrane and dissociates from the membrane upon phosphorylation. Ras-associated protein 1 recruits this protein to coat protein complex II (COPII) vesicles during budding from the endoplasmic reticulum, where it interacts with a set of COPII vesicle-associated SNAREs to form a cis-SNARE complex that promotes targeting to the Golgi apparatus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]
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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=-0.92).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
USO1 | NM_003715.4 | c.1987-194G>A | intron_variant | ENST00000514213.7 | NP_003706.2 | |||
USO1 | NM_001290049.2 | c.2020-194G>A | intron_variant | NP_001276978.1 | ||||
USO1 | XM_006714396.5 | c.2008-194G>A | intron_variant | XP_006714459.1 | ||||
USO1 | XM_006714397.4 | c.1999-194G>A | intron_variant | XP_006714460.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
USO1 | ENST00000514213.7 | c.1987-194G>A | intron_variant | 1 | NM_003715.4 | ENSP00000444850.2 | ||||
USO1 | ENST00000264904.8 | c.2020-194G>A | intron_variant | 2 | ENSP00000264904.7 |
Frequencies
GnomAD3 genomes AF: 0.535 AC: 81175AN: 151780Hom.: 23440 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.535 AC: 81196AN: 151898Hom.: 23440 Cov.: 31 AF XY: 0.537 AC XY: 39874AN XY: 74240
GnomAD4 genome
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ClinVar
Not reported inComputational scores
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Name
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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