chr2-144387062-T-TAC
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_014795.4(ZEB2):c.*2388_*2389insGT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00683 in 146,188 control chromosomes in the GnomAD database, including 4 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.0068 ( 4 hom., cov: 26)
Failed GnomAD Quality Control
Consequence
ZEB2
NM_014795.4 3_prime_UTR
NM_014795.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.439
Genes affected
ZEB2 (HGNC:14881): (zinc finger E-box binding homeobox 2) The protein encoded by this gene is a member of the Zfh1 family of 2-handed zinc finger/homeodomain proteins. It is located in the nucleus and functions as a DNA-binding transcriptional repressor that interacts with activated SMADs. Mutations in this gene are associated with Hirschsprung disease/Mowat-Wilson syndrome. Alternatively spliced transcript variants have been found for this gene.[provided by RefSeq, Jan 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP6
Variant 2-144387062-T-TAC is Benign according to our data. Variant chr2-144387062-T-TAC is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 331265.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Benign=1}.
BS2
High AC in GnomAd4 at 999 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZEB2 | NM_014795.4 | c.*2388_*2389insGT | 3_prime_UTR_variant | 10/10 | ENST00000627532.3 | ||
ZEB2 | NM_001171653.2 | c.*2388_*2389insGT | 3_prime_UTR_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZEB2 | ENST00000627532.3 | c.*2388_*2389insGT | 3_prime_UTR_variant | 10/10 | 1 | NM_014795.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00683 AC: 998AN: 146106Hom.: 4 Cov.: 26
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GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 exome
Data not reliable, filtered out with message: AC0
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GnomAD4 genome AF: 0.00683 AC: 999AN: 146188Hom.: 4 Cov.: 26 AF XY: 0.00634 AC XY: 452AN XY: 71318
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Mowat-Wilson syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | ZEB2: BS1, BS2 - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at