rs567229506
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_014795.4(ZEB2):c.*35delT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000746 in 1,580,884 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in Lovd as Benign (no stars).
Frequency
Genomes: 𝑓 0.00015 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000067 ( 0 hom. )
Consequence
ZEB2
NM_014795.4 3_prime_UTR
NM_014795.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.27
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 2-144389415-GA-G is Benign according to our data. Variant chr2-144389415-GA-G is described in Lovd as [Benign].
BS2
High AC in GnomAd4 at 22 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000147 AC: 22AN: 150064Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.0000671 AC: 96AN: 1430704Hom.: 0 Cov.: 30 AF XY: 0.0000757 AC XY: 54AN XY: 713092
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GnomAD4 genome AF: 0.000146 AC: 22AN: 150180Hom.: 0 Cov.: 32 AF XY: 0.000109 AC XY: 8AN XY: 73228
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ClinVar
Not reported inComputational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at