chr2-144400257-G-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_014795.4(ZEB2):c.930C>T(p.Tyr310Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0027 in 1,609,982 control chromosomes in the GnomAD database, including 53 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_014795.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0103 AC: 1572AN: 152198Hom.: 26 Cov.: 32
GnomAD3 exomes AF: 0.00393 AC: 963AN: 245024Hom.: 15 AF XY: 0.00318 AC XY: 425AN XY: 133444
GnomAD4 exome AF: 0.00190 AC: 2768AN: 1457666Hom.: 27 Cov.: 32 AF XY: 0.00176 AC XY: 1277AN XY: 725310
GnomAD4 genome AF: 0.0103 AC: 1574AN: 152316Hom.: 26 Cov.: 32 AF XY: 0.0105 AC XY: 783AN XY: 74486
ClinVar
Submissions by phenotype
not specified Benign:3
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. -
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not provided Benign:3
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ZEB2: BP4, BP7 -
Mowat-Wilson syndrome Benign:2
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Inborn genetic diseases Benign:1
This alteration is classified as 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