rs730881184
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4_ModerateBP6_Very_Strong
The NM_014795.4(ZEB2):c.139G>T(p.Ala47Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000041 in 1,461,634 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A47A) has been classified as Likely benign.
Frequency
Consequence
NM_014795.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZEB2 | NM_014795.4 | c.139G>T | p.Ala47Ser | missense_variant | 3/10 | ENST00000627532.3 | |
ZEB2 | NM_001171653.2 | c.139G>T | p.Ala47Ser | missense_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZEB2 | ENST00000627532.3 | c.139G>T | p.Ala47Ser | missense_variant | 3/10 | 1 | NM_014795.4 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 251016Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135666
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461634Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727126
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Mowat-Wilson syndrome Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 07, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 07, 2021 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 14, 2014 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at