rs6132976
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000380445.8(VPS16):c.53+3578G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0391 in 152,190 control chromosomes in the GnomAD database, including 231 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 0.039 ( 231 hom., cov: 32)
Consequence
VPS16
ENST00000380445.8 intron
ENST00000380445.8 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.473
Genes affected
VPS16 (HGNC:14584): (VPS16 core subunit of CORVET and HOPS complexes) 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 homolog of yeast class C Vps16 protein. The mammalian class C Vps proteins are predominantly associated with late endosomes/lysosomes, and like their yeast counterparts, may mediate vesicle trafficking steps in the endosome/lysosome pathway. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2009]
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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=-0.83).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VPS16 | NM_022575.4 | c.53+3578G>A | intron_variant | ENST00000380445.8 | NP_072097.2 | |||
VPS16 | NM_080413.3 | c.53+3578G>A | intron_variant | NP_536338.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VPS16 | ENST00000380445.8 | c.53+3578G>A | intron_variant | 1 | NM_022575.4 | ENSP00000369810 | P1 | |||
VPS16 | ENST00000380469.7 | c.53+3578G>A | intron_variant | 2 | ENSP00000369836 | |||||
VPS16 | ENST00000417508.1 | c.-75+3578G>A | intron_variant | 5 | ENSP00000409840 | |||||
VPS16 | ENST00000453689.5 | c.-75+3578G>A | intron_variant | 3 | ENSP00000417031 |
Frequencies
GnomAD3 genomes AF: 0.0389 AC: 5921AN: 152074Hom.: 221 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0391 AC: 5948AN: 152190Hom.: 231 Cov.: 32 AF XY: 0.0409 AC XY: 3046AN XY: 74406
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3478
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