rs143450927
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_014795.4(ZEB2):c.3067+6A>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0045 in 1,612,920 control chromosomes in the GnomAD database, including 314 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_014795.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZEB2 | NM_014795.4 | c.3067+6A>T | splice_region_variant, intron_variant | ENST00000627532.3 | NP_055610.1 | |||
ZEB2 | NM_001171653.2 | c.2995+6A>T | splice_region_variant, intron_variant | NP_001165124.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZEB2 | ENST00000627532.3 | c.3067+6A>T | splice_region_variant, intron_variant | 1 | NM_014795.4 | ENSP00000487174.1 |
Frequencies
GnomAD3 genomes AF: 0.00715 AC: 1088AN: 152232Hom.: 40 Cov.: 32
GnomAD3 exomes AF: 0.0173 AC: 4349AN: 251452Hom.: 227 AF XY: 0.0132 AC XY: 1789AN XY: 135902
GnomAD4 exome AF: 0.00422 AC: 6160AN: 1460570Hom.: 273 Cov.: 32 AF XY: 0.00364 AC XY: 2645AN XY: 726626
GnomAD4 genome AF: 0.00717 AC: 1092AN: 152350Hom.: 41 Cov.: 32 AF XY: 0.00776 AC XY: 578AN XY: 74500
ClinVar
Submissions by phenotype
not specified Benign:6
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 11, 2012 | 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. - |
Benign, no assertion criteria provided | clinical testing | Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia | Jan 30, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Dec 17, 2013 | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Benign, criteria provided, single submitter | clinical testing | Molecular Genetics Laboratory, Children's Mercy Hospital and Clinics | Mar 02, 2015 | This variant was interpreted as benign based on ACMG evidence categories BS1 BS2. - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jul 31, 2024 | - - |
Mowat-Wilson syndrome Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 10, 2013 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 07, 2021 | - - |
not provided Benign:3
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Dec 09, 2014 | - - |
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at