16-89709365-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004913.3(VPS9D1):c.1459G>A(p.Ala487Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000953 in 1,573,164 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. 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 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VPS9D1 | ENST00000389386.8 | c.1459G>A | p.Ala487Thr | missense_variant | Exon 12 of 15 | 1 | NM_004913.3 | ENSP00000374037.3 | ||
VPS9D1 | ENST00000561976.5 | c.1249G>A | p.Ala417Thr | missense_variant | Exon 11 of 14 | 1 | ENSP00000454244.1 | |||
VPS9D1 | ENST00000565023.1 | c.259G>A | p.Ala87Thr | missense_variant | Exon 3 of 6 | 5 | ENSP00000455792.1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151960Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000192 AC: 4AN: 208714Hom.: 0 AF XY: 0.0000177 AC XY: 2AN XY: 113218
GnomAD4 exome AF: 0.00000985 AC: 14AN: 1421204Hom.: 0 Cov.: 32 AF XY: 0.0000142 AC XY: 10AN XY: 704306
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151960Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74198
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1459G>A (p.A487T) alteration is located in exon 12 (coding exon 12) of the VPS9D1 gene. This alteration results from a G to A substitution at nucleotide position 1459, causing the alanine (A) at amino acid position 487 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