16-89709810-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004913.3(VPS9D1):c.1355C>T(p.Ser452Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00000434 in 1,613,616 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 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 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VPS9D1 | ENST00000389386.8 | c.1355C>T | p.Ser452Phe | missense_variant | Exon 11 of 15 | 1 | NM_004913.3 | ENSP00000374037.3 | ||
VPS9D1 | ENST00000561976.5 | c.1145C>T | p.Ser382Phe | missense_variant | Exon 10 of 14 | 1 | ENSP00000454244.1 | |||
VPS9D1 | ENST00000565023.1 | c.155C>T | p.Ser52Phe | missense_variant | Exon 2 of 6 | 5 | ENSP00000455792.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152078Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249224Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135264
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461538Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727092
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152078Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74300
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1355C>T (p.S452F) alteration is located in exon 11 (coding exon 11) of the VPS9D1 gene. This alteration results from a C to T substitution at nucleotide position 1355, causing the serine (S) at amino acid position 452 to be replaced by a phenylalanine (F). 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