16-89708455-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_004913.3(VPS9D1):c.1774G>A(p.Ala592Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000105 in 1,612,654 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
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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.1774G>A | p.Ala592Thr | missense_variant | Exon 14 of 15 | 1 | NM_004913.3 | ENSP00000374037.3 | ||
VPS9D1 | ENST00000561976.5 | c.1564G>A | p.Ala522Thr | missense_variant | Exon 13 of 14 | 1 | ENSP00000454244.1 | |||
VPS9D1 | ENST00000565023.1 | c.574G>A | p.Ala192Thr | missense_variant | Exon 5 of 6 | 5 | ENSP00000455792.1 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152264Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000984 AC: 24AN: 243812Hom.: 0 AF XY: 0.000113 AC XY: 15AN XY: 133240
GnomAD4 exome AF: 0.000105 AC: 154AN: 1460390Hom.: 0 Cov.: 32 AF XY: 0.000116 AC XY: 84AN XY: 726488
GnomAD4 genome AF: 0.000105 AC: 16AN: 152264Hom.: 0 Cov.: 34 AF XY: 0.000108 AC XY: 8AN XY: 74390
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1774G>A (p.A592T) 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 1774, causing the alanine (A) at amino acid position 592 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