X-80022027-TACACACACACACACACACACAC-TACACACAC
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NM_001109878.2(TBX22):c.-2-213_-2-200delCACACACACACACA 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 0.0052 ( 2 hom., 110 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 = 0.00516 (480/92961) while in subpopulation AFR AF= 0.0172 (445/25914). AF 95% confidence interval is 0.0159. There are 2 homozygotes in gnomad4. There are 110 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 2 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TBX22 | NM_001109878.2 | c.-2-213_-2-200delCACACACACACACA | intron_variant | Intron 1 of 8 | ENST00000373296.8 | NP_001103348.1 | ||
TBX22 | NM_001109879.2 | c.-358-213_-358-200delCACACACACACACA | 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_-2-227delACACACACACACAC | intron_variant | Intron 1 of 8 | 5 | NM_001109878.2 | ENSP00000362393.3 | |||
TBX22 | ENST00000476373.1 | n.120-240_120-227delACACACACACACAC | intron_variant | Intron 1 of 1 | 3 | |||||
TBX22 | ENST00000626498.2 | n.-2-240_-2-227delACACACACACACAC | intron_variant | Intron 1 of 8 | 2 | ENSP00000487527.1 |
Frequencies
GnomAD3 genomes AF: 0.00515 AC: 479AN: 92944Hom.: 2 Cov.: 0 AF XY: 0.00543 AC XY: 109AN XY: 20068
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GnomAD4 genome AF: 0.00516 AC: 480AN: 92961Hom.: 2 Cov.: 0 AF XY: 0.00547 AC XY: 110AN XY: 20095
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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