16-89708467-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_004913.3(VPS9D1):c.1762G>A(p.Val588Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000769 in 1,613,088 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004913.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VPS9D1 | ENST00000389386.8 | c.1762G>A | p.Val588Met | missense_variant | Exon 14 of 15 | 1 | NM_004913.3 | ENSP00000374037.3 | ||
VPS9D1 | ENST00000561976.5 | c.1552G>A | p.Val518Met | missense_variant | Exon 13 of 14 | 1 | ENSP00000454244.1 | |||
VPS9D1 | ENST00000565023.1 | c.562G>A | p.Val188Met | missense_variant | Exon 5 of 6 | 5 | ENSP00000455792.1 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152256Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000980 AC: 24AN: 244880Hom.: 0 AF XY: 0.000127 AC XY: 17AN XY: 133736
GnomAD4 exome AF: 0.0000719 AC: 105AN: 1460714Hom.: 0 Cov.: 32 AF XY: 0.0000798 AC XY: 58AN XY: 726674
GnomAD4 genome AF: 0.000125 AC: 19AN: 152374Hom.: 0 Cov.: 34 AF XY: 0.0000671 AC XY: 5AN XY: 74508
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1762G>A (p.V588M) alteration is located in exon 14 (coding exon 14) of the VPS9D1 gene. This alteration results from a G to A substitution at nucleotide position 1762, causing the valine (V) at amino acid position 588 to be replaced by a methionine (M). 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