6-33264879-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_022553.6(VPS52):c.1303G>A(p.Ala435Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,612,826 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022553.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VPS52 | NM_022553.6 | c.1303G>A | p.Ala435Thr | missense_variant | 13/20 | ENST00000445902.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VPS52 | ENST00000445902.3 | c.1303G>A | p.Ala435Thr | missense_variant | 13/20 | 1 | NM_022553.6 | P1 | |
VPS52 | ENST00000482399.5 | c.*1432G>A | 3_prime_UTR_variant | 12/19 | 2 | ||||
VPS52 | ENST00000478934.5 | n.1164G>A | non_coding_transcript_exon_variant | 11/18 | 2 | ||||
VPS52 | ENST00000493379.1 | n.256G>A | non_coding_transcript_exon_variant | 3/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152112Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460714Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 726684
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152112Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 27, 2022 | The c.1303G>A (p.A435T) alteration is located in exon 13 (coding exon 13) of the VPS52 gene. This alteration results from a G to A substitution at nucleotide position 1303, causing the alanine (A) at amino acid position 435 to be replaced by a threonine (T). 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