X-80022128-GGTTTTGTTTT-GGTTTTGTTTTGTTTT
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NM_001109878.2(TBX22):c.-2-119_-2-115dupGTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000223 in 552,501 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 34 hemizygotes in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00019 ( 0 hom., 4 hem., cov: 7)
Exomes 𝑓: 0.00023 ( 0 hom. 30 hem. )
Consequence
TBX22
NM_001109878.2 intron
NM_001109878.2 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.183
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 eas. gnomad4 allele frequency = 0.000187 (20/106765) while in subpopulation EAS AF= 0.00122 (4/3276). AF 95% confidence interval is 0.000416. There are 0 homozygotes in gnomad4. There are 4 alleles in male gnomad4 subpopulation. Median coverage is 7. This position pass quality control queck.
BS2
High Hemizygotes in GnomAd4 at 4 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TBX22 | NM_001109878.2 | c.-2-119_-2-115dupGTTTT | intron_variant | Intron 1 of 8 | ENST00000373296.8 | NP_001103348.1 | ||
TBX22 | NM_001109879.2 | c.-358-119_-358-115dupGTTTT | 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.-2-140_-2-139insGTTTT | intron_variant | Intron 1 of 8 | 5 | NM_001109878.2 | ENSP00000362393.3 | |||
TBX22 | ENST00000476373.1 | n.120-140_120-139insGTTTT | intron_variant | Intron 1 of 1 | 3 | |||||
TBX22 | ENST00000626498.2 | n.-2-140_-2-139insGTTTT | intron_variant | Intron 1 of 8 | 2 | ENSP00000487527.1 |
Frequencies
GnomAD3 genomes AF: 0.000187 AC: 20AN: 106765Hom.: 0 Cov.: 7 AF XY: 0.000135 AC XY: 4AN XY: 29543
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GnomAD4 exome AF: 0.000231 AC: 103AN: 445736Hom.: 0 AF XY: 0.000216 AC XY: 30AN XY: 139198
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GnomAD4 genome AF: 0.000187 AC: 20AN: 106765Hom.: 0 Cov.: 7 AF XY: 0.000135 AC XY: 4AN XY: 29543
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at