rs201610914
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004913.3(VPS9D1):c.1532C>T(p.Ala511Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000132 in 1,609,512 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_004913.3 missense
Scores
Clinical Significance
Conservation
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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.1532C>T | p.Ala511Val | missense_variant | Exon 12 of 15 | 1 | NM_004913.3 | ENSP00000374037.3 | ||
VPS9D1 | ENST00000561976.5 | c.1322C>T | p.Ala441Val | missense_variant | Exon 11 of 14 | 1 | ENSP00000454244.1 | |||
VPS9D1 | ENST00000565023.1 | c.332C>T | p.Ala111Val | missense_variant | Exon 3 of 6 | 5 | ENSP00000455792.1 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152150Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000112 AC: 27AN: 240782Hom.: 0 AF XY: 0.000121 AC XY: 16AN XY: 131880
GnomAD4 exome AF: 0.000135 AC: 197AN: 1457362Hom.: 1 Cov.: 32 AF XY: 0.000121 AC XY: 88AN XY: 725060
GnomAD4 genome AF: 0.000105 AC: 16AN: 152150Hom.: 0 Cov.: 31 AF XY: 0.000121 AC XY: 9AN XY: 74314
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at