rs10779958
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_181575.5(AUP1):c.524+100T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 1,425,506 control chromosomes in the GnomAD database, including 49,073 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 0.32 ( 11582 hom., cov: 33)
Exomes 𝑓: 0.20 ( 37491 hom. )
Consequence
AUP1
NM_181575.5 intron
NM_181575.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.662
Genes affected
AUP1 (HGNC:891): (AUP1 lipid droplet regulating VLDL assembly factor) The protein encoded this gene is involved in several pathways including quality control of misfolded proteins in the endoplasmic reticulum and lipid droplet accumulation. Lipid droplets are organelles in the cytoplasm that store neutral lipids such as cholesterol esters and trigylycerides to prevent the overabundance of free cholesterol and fatty acids in cells, but also to act as storage for other metabolic processes, such as membrane biogenesis. Reduced expression of this gene results in reduced lipid droplet clustering, a function that is dependent on ubiquitination of the protein. This protein contains multiple domains including a hydrophobic N-terminal domain, an acetyltranferase domain, a ubiquitin-binding CUE domain, and a UBE2B2-binding domain (G2BR). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 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=-0.8).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AUP1 | NM_181575.5 | c.524+100T>G | intron_variant | ENST00000377526.4 | |||
AUP1 | NR_126510.2 | n.601+100T>G | intron_variant, non_coding_transcript_variant | ||||
AUP1 | NR_126511.2 | n.797+100T>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AUP1 | ENST00000377526.4 | c.524+100T>G | intron_variant | 1 | NM_181575.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.321 AC: 48797AN: 152008Hom.: 11557 Cov.: 33
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GnomAD4 exome AF: 0.196 AC: 249498AN: 1273380Hom.: 37491 Cov.: 19 AF XY: 0.197 AC XY: 124890AN XY: 634670
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GnomAD4 genome ? AF: 0.321 AC: 48869AN: 152126Hom.: 11582 Cov.: 33 AF XY: 0.323 AC XY: 24014AN XY: 74408
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ClinVar
Not reported inComputational 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