chr16-69321142-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_013245.3(VPS4A):c.943A>G(p.Thr315Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T315M) has been classified as Uncertain significance.
Frequency
Consequence
NM_013245.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VPS4A | NM_013245.3 | c.943A>G | p.Thr315Ala | missense_variant | 9/11 | ENST00000254950.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VPS4A | ENST00000254950.13 | c.943A>G | p.Thr315Ala | missense_variant | 9/11 | 1 | NM_013245.3 | P1 | |
VPS4A | ENST00000564399.1 | n.50A>G | non_coding_transcript_exon_variant | 1/2 | 5 | ||||
COG8 | ENST00000564419.1 | n.30-96T>C | intron_variant, non_coding_transcript_variant | 5 | |||||
VPS4A | ENST00000562754.1 | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1436716Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 712312
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Sep 09, 2022 | Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.