3-184834695-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001009921.3(VPS8):c.400C>T(p.Arg134Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000128 in 1,562,708 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R134H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001009921.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VPS8 | NM_001009921.3 | c.400C>T | p.Arg134Cys | missense_variant | 5/48 | ENST00000625842.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VPS8 | ENST00000625842.3 | c.400C>T | p.Arg134Cys | missense_variant | 5/48 | 5 | NM_001009921.3 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000330 AC: 5AN: 151640Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000106 AC: 15AN: 1411068Hom.: 0 Cov.: 32 AF XY: 0.0000115 AC XY: 8AN XY: 696942
GnomAD4 genome AF: 0.0000330 AC: 5AN: 151640Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74038
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 22, 2022 | The c.400C>T (p.R134C) alteration is located in exon 5 (coding exon 4) of the VPS8 gene. This alteration results from a C to T substitution at nucleotide position 400, causing the arginine (R) at amino acid position 134 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at