6-33266665-G-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_022553.6(VPS52):c.1173C>T(p.Asp391=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00262 in 1,612,922 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0017 ( 2 hom., cov: 31)
Exomes 𝑓: 0.0027 ( 14 hom. )
Consequence
VPS52
NM_022553.6 synonymous
NM_022553.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.79
Genes affected
VPS52 (HGNC:10518): (VPS52 subunit of GARP complex) This gene encodes a protein that is similar to the yeast suppressor of actin mutations 2 gene. The yeast protein forms a subunit of the tetrameric Golgi-associated retrograde protein complex that is involved in vesicle trafficking from from both early and late endosomes, back to the trans-Golgi network. This gene is located on chromosome 6 in a head-to-head orientation with the gene encoding ribosomal protein S18. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BP6
?
Variant 6-33266665-G-A is Benign according to our data. Variant chr6-33266665-G-A is described in ClinVar as [Benign]. Clinvar id is 770362.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VPS52 | NM_022553.6 | c.1173C>T | p.Asp391= | synonymous_variant | 12/20 | ENST00000445902.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VPS52 | ENST00000445902.3 | c.1173C>T | p.Asp391= | synonymous_variant | 12/20 | 1 | NM_022553.6 | P1 | |
VPS52 | ENST00000482399.5 | c.*1302C>T | 3_prime_UTR_variant | 11/19 | 2 | ||||
VPS52 | ENST00000478934.5 | n.1034C>T | non_coding_transcript_exon_variant | 10/18 | 2 | ||||
VPS52 | ENST00000493379.1 | n.126C>T | non_coding_transcript_exon_variant | 2/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00172 AC: 262AN: 152120Hom.: 2 Cov.: 31
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GnomAD3 exomes AF: 0.00151 AC: 372AN: 246454Hom.: 1 AF XY: 0.00156 AC XY: 210AN XY: 134322
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GnomAD4 exome AF: 0.00271 AC: 3959AN: 1460684Hom.: 14 Cov.: 31 AF XY: 0.00263 AC XY: 1911AN XY: 726664
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GnomAD4 genome ? AF: 0.00172 AC: 262AN: 152238Hom.: 2 Cov.: 31 AF XY: 0.00144 AC XY: 107AN XY: 74440
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 10, 2018 | - - |
Computational scores
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Benign
CADD
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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