2-144399347-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_014795.4(ZEB2):c.1840C>T(p.Leu614=) variant causes a synonymous change. The variant allele was found at a frequency of 0.000677 in 1,614,176 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts 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. L614L) has been classified as Likely benign.
Frequency
Consequence
NM_014795.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZEB2 | NM_014795.4 | c.1840C>T | p.Leu614= | synonymous_variant | 8/10 | ENST00000627532.3 | |
ZEB2 | NM_001171653.2 | c.1768C>T | p.Leu590= | synonymous_variant | 7/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZEB2 | ENST00000627532.3 | c.1840C>T | p.Leu614= | synonymous_variant | 8/10 | 1 | NM_014795.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000394 AC: 60AN: 152188Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000160 AC: 40AN: 250522Hom.: 0 AF XY: 0.000163 AC XY: 22AN XY: 135346
GnomAD4 exome AF: 0.000706 AC: 1032AN: 1461870Hom.: 19 Cov.: 32 AF XY: 0.000705 AC XY: 513AN XY: 727234
GnomAD4 genome AF: 0.000394 AC: 60AN: 152306Hom.: 1 Cov.: 32 AF XY: 0.000389 AC XY: 29AN XY: 74478
ClinVar
Submissions by phenotype
Mowat-Wilson syndrome Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 18, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 17, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 07, 2021 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 23, 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. - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 26, 2017 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at