rs1267724404
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004913.3(VPS9D1):āc.1549G>Cā(p.Gly517Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,611,132 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. 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.1549G>C | p.Gly517Arg | missense_variant | Exon 12 of 15 | 1 | NM_004913.3 | ENSP00000374037.3 | ||
VPS9D1 | ENST00000561976.5 | c.1339G>C | p.Gly447Arg | missense_variant | Exon 11 of 14 | 1 | ENSP00000454244.1 | |||
VPS9D1 | ENST00000565023.1 | c.349G>C | p.Gly117Arg | missense_variant | Exon 3 of 6 | 5 | ENSP00000455792.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152132Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000826 AC: 2AN: 242032Hom.: 0 AF XY: 0.0000151 AC XY: 2AN XY: 132622
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1459000Hom.: 0 Cov.: 32 AF XY: 0.00000551 AC XY: 4AN XY: 725868
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152132Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74314
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at