16-89708452-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_004913.3(VPS9D1):c.1777G>T(p.Ala593Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000118 in 1,612,536 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004913.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VPS9D1 | ENST00000389386.8 | c.1777G>T | p.Ala593Ser | missense_variant | Exon 14 of 15 | 1 | NM_004913.3 | ENSP00000374037.3 | ||
VPS9D1 | ENST00000561976.5 | c.1567G>T | p.Ala523Ser | missense_variant | Exon 13 of 14 | 1 | ENSP00000454244.1 | |||
VPS9D1 | ENST00000565023.1 | c.577G>T | p.Ala193Ser | missense_variant | Exon 5 of 6 | 5 | ENSP00000455792.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152244Hom.: 0 Cov.: 34
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1460292Hom.: 0 Cov.: 32 AF XY: 0.00000826 AC XY: 6AN XY: 726438
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152244Hom.: 0 Cov.: 34 AF XY: 0.0000134 AC XY: 1AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1777G>T (p.A593S) alteration is located in exon 14 (coding exon 14) of the VPS9D1 gene. This alteration results from a G to T substitution at nucleotide position 1777, causing the alanine (A) at amino acid position 593 to be replaced by a serine (S). 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