rs11773094
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014396.4(VPS41):c.*1170G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 152,156 control chromosomes in the GnomAD database, including 7,768 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 0.29 ( 7766 hom., cov: 33)
Exomes 𝑓: 0.50 ( 2 hom. )
Consequence
VPS41
NM_014396.4 3_prime_UTR
NM_014396.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.31
Genes affected
VPS41 (HGNC:12713): (VPS41 subunit of HOPS complex) Vesicle mediated protein sorting plays an important role in segregation of intracellular molecules into distinct organelles. Genetic studies in yeast have identified more than 40 vacuolar protein sorting (VPS) genes involved in vesicle transport to vacuoles. This gene encodes the human ortholog of yeast Vps41 protein which is also conserved in Drosophila, tomato, and Arabidopsis. Expression studies in yeast and human indicate that this protein may be involved in the formation and fusion of transport vesicles from the Golgi. Several transcript variants encoding different isoforms have been described for this gene, however, the full-length nature of not all is known. [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=-0.97).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VPS41 | NM_014396.4 | c.*1170G>A | 3_prime_UTR_variant | 29/29 | ENST00000310301.9 | ||
VPS41 | NM_080631.4 | c.*1170G>A | 3_prime_UTR_variant | 28/28 | |||
VPS41 | XM_017011988.2 | c.*1170G>A | 3_prime_UTR_variant | 16/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VPS41 | ENST00000310301.9 | c.*1170G>A | 3_prime_UTR_variant | 29/29 | 1 | NM_014396.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.288 AC: 43823AN: 152012Hom.: 7766 Cov.: 33
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GnomAD4 exome AF: 0.500 AC: 13AN: 26Hom.: 2 Cov.: 0 AF XY: 0.500 AC XY: 10AN XY: 20
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GnomAD4 genome ? AF: 0.288 AC: 43818AN: 152130Hom.: 7766 Cov.: 33 AF XY: 0.285 AC XY: 21191AN XY: 74368
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ClinVar
Not reported inComputational scores
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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