20-2840955-C-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_022575.4(VPS16):c.53+128C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 907,542 control chromosomes in the GnomAD database, including 14,465 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.22 ( 5352 hom., cov: 32)
Exomes 𝑓: 0.14 ( 9113 hom. )
Consequence
VPS16
NM_022575.4 intron
NM_022575.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.567
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]
PCED1A (HGNC:16212): (PC-esterase domain containing 1A) The protein encoded by this gene is a member of the GDSL/SGNH superfamily. Members of this family are hydrolytic enzymes with esterase and lipase activity and broad substrate specificity. This protein belongs to the Pmr5-Cas1p-esterase subfamily in that it contains the catalytic triad comprised of serine, aspartate and histidine and lacks two conserved regions (glycine after strand S2 and GxND motif). A pseudogene of this gene has been identified on the long arm of chromosome 2. Alternative splicing results in multiple transcript variants that encode different protein isoforms. [provided by RefSeq, Sep 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 20-2840955-C-T is Benign according to our data. Variant chr20-2840955-C-T is described in ClinVar as [Benign]. Clinvar id is 1286534.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VPS16 | NM_022575.4 | c.53+128C>T | intron_variant | ENST00000380445.8 | NP_072097.2 | |||
PCED1A | NM_001271168.2 | c.-111G>A | 5_prime_UTR_variant | 1/8 | NP_001258097.1 | |||
PCED1A | XM_005260804.3 | c.-111G>A | 5_prime_UTR_variant | 1/8 | XP_005260861.1 | |||
VPS16 | NM_080413.3 | c.53+128C>T | intron_variant | NP_536338.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VPS16 | ENST00000380445.8 | c.53+128C>T | intron_variant | 1 | NM_022575.4 | ENSP00000369810 | P1 |
Frequencies
GnomAD3 genomes AF: 0.224 AC: 34080AN: 152028Hom.: 5348 Cov.: 32
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GnomAD4 exome AF: 0.143 AC: 108374AN: 755402Hom.: 9113 Cov.: 10 AF XY: 0.140 AC XY: 53922AN XY: 383930
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GnomAD4 genome AF: 0.224 AC: 34108AN: 152140Hom.: 5352 Cov.: 32 AF XY: 0.221 AC XY: 16445AN XY: 74394
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 17, 2021 | - - |
Computational scores
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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