16-89708926-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_004913.3(VPS9D1):c.1628C>T(p.Ala543Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000811 in 1,603,946 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.1628C>T | p.Ala543Val | missense_variant | Exon 13 of 15 | 1 | NM_004913.3 | ENSP00000374037.3 | ||
VPS9D1 | ENST00000561976.5 | c.1418C>T | p.Ala473Val | missense_variant | Exon 12 of 14 | 1 | ENSP00000454244.1 | |||
VPS9D1 | ENST00000565023.1 | c.428C>T | p.Ala143Val | missense_variant | Exon 4 of 6 | 5 | ENSP00000455792.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152154Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000872 AC: 2AN: 229352Hom.: 0 AF XY: 0.0000159 AC XY: 2AN XY: 126066
GnomAD4 exome AF: 0.00000827 AC: 12AN: 1451792Hom.: 0 Cov.: 33 AF XY: 0.00000970 AC XY: 7AN XY: 721838
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152154Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1628C>T (p.A543V) alteration is located in exon 13 (coding exon 13) of the VPS9D1 gene. This alteration results from a C to T substitution at nucleotide position 1628, causing the alanine (A) at amino acid position 543 to be replaced by a valine (V). 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