chr20-41202422-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001384317.1(ZHX3):c.2495G>A(p.Arg832Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000159 in 1,614,142 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001384317.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZHX3 | NM_001384317.1 | c.2495G>A | p.Arg832Gln | missense_variant | 3/4 | ENST00000683867.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZHX3 | ENST00000683867.1 | c.2495G>A | p.Arg832Gln | missense_variant | 3/4 | NM_001384317.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152148Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000119 AC: 30AN: 251256Hom.: 0 AF XY: 0.000110 AC XY: 15AN XY: 135826
GnomAD4 exome AF: 0.000162 AC: 237AN: 1461876Hom.: 0 Cov.: 31 AF XY: 0.000140 AC XY: 102AN XY: 727242
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152266Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74474
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Apr 15, 2022 | This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 832 of the ZHX3 protein (p.Arg832Gln). This variant is present in population databases (rs200260351, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with ZHX3-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at