X-80022027-TACACACACACACACACACACAC-TACACACACAC
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NM_001109878.2(TBX22):c.-2-211_-2-200delCACACACACACA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00044 ( 0 hom., 7 hem., cov: 0)
Consequence
TBX22
NM_001109878.2 intron
NM_001109878.2 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.750
Genes affected
TBX22 (HGNC:11600): (T-box transcription factor 22) This gene is a member of a phylogenetically conserved family of genes that share a common DNA-binding domain, the T-box. T-box genes encode transcription factors involved in the regulation of developmental processes. Mutations in this gene have been associated with the inherited X-linked disorder, Cleft palate with ankyloglossia, and it is believed to play a major role in human palatogenesis. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000441 (41/92964) while in subpopulation AFR AF= 0.00081 (21/25920). AF 95% confidence interval is 0.000542. There are 0 homozygotes in gnomad4. There are 7 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High Hemizygotes in GnomAd4 at 7 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TBX22 | NM_001109878.2 | c.-2-211_-2-200delCACACACACACA | intron_variant | Intron 1 of 8 | ENST00000373296.8 | NP_001103348.1 | ||
TBX22 | NM_001109879.2 | c.-358-211_-358-200delCACACACACACA | intron_variant | Intron 1 of 8 | NP_001103349.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TBX22 | ENST00000373296.8 | c.-2-240_-2-229delACACACACACAC | intron_variant | Intron 1 of 8 | 5 | NM_001109878.2 | ENSP00000362393.3 | |||
TBX22 | ENST00000476373.1 | n.120-240_120-229delACACACACACAC | intron_variant | Intron 1 of 1 | 3 | |||||
TBX22 | ENST00000626498.2 | n.-2-240_-2-229delACACACACACAC | intron_variant | Intron 1 of 8 | 2 | ENSP00000487527.1 |
Frequencies
GnomAD3 genomes AF: 0.000430 AC: 40AN: 92946Hom.: 0 Cov.: 0 AF XY: 0.000349 AC XY: 7AN XY: 20070
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GnomAD4 genome AF: 0.000441 AC: 41AN: 92964Hom.: 0 Cov.: 0 AF XY: 0.000348 AC XY: 7AN XY: 20098
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ClinVar
Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at