16-89709254-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_004913.3(VPS9D1):āc.1570T>Cā(p.Cys524Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000726 in 1,459,618 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 (ā ).
Frequency
Consequence
NM_004913.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VPS9D1 | ENST00000389386.8 | c.1570T>C | p.Cys524Arg | missense_variant | Exon 12 of 15 | 1 | NM_004913.3 | ENSP00000374037.3 | ||
VPS9D1 | ENST00000561976.5 | c.1360T>C | p.Cys454Arg | missense_variant | Exon 11 of 14 | 1 | ENSP00000454244.1 | |||
VPS9D1 | ENST00000565023.1 | c.370T>C | p.Cys124Arg | missense_variant | Exon 3 of 6 | 5 | ENSP00000455792.1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000412 AC: 1AN: 242602Hom.: 0 AF XY: 0.00000752 AC XY: 1AN XY: 133016
GnomAD4 exome AF: 0.0000726 AC: 106AN: 1459618Hom.: 0 Cov.: 33 AF XY: 0.0000689 AC XY: 50AN XY: 726128
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1570T>C (p.C524R) alteration is located in exon 12 (coding exon 12) of the VPS9D1 gene. This alteration results from a T to C substitution at nucleotide position 1570, causing the cysteine (C) at amino acid position 524 to be replaced by an arginine (R). 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