chr3-114339115-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_001348800.3(ZBTB20):c.2116G>A(p.Val706Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000162 in 1,608,922 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 (★). Synonymous variant affecting the same amino acid position (i.e. V706V) has been classified as Likely benign.
Frequency
Consequence
NM_001348800.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZBTB20 | NM_001348800.3 | c.2116G>A | p.Val706Met | missense_variant | 12/12 | ENST00000675478.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZBTB20 | ENST00000675478.1 | c.2116G>A | p.Val706Met | missense_variant | 12/12 | NM_001348800.3 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152234Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000243 AC: 6AN: 246898Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 133296
GnomAD4 exome AF: 0.0000172 AC: 25AN: 1456688Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 14AN XY: 724144
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152234Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74370
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Sep 27, 2023 | 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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on ZBTB20 protein function. This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 706 of the ZBTB20 protein (p.Val706Met). This variant is present in population databases (rs769253978, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with ZBTB20-related conditions. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at