X-80022027-TACACACACACACACACACACAC-TACACACACACACACACACACACACACAC
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_001109878.2(TBX22):c.-2-205_-2-200dupCACACA 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 0.016 ( 21 hom., 256 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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0539 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TBX22 | NM_001109878.2 | c.-2-205_-2-200dupCACACA | intron_variant | Intron 1 of 8 | ENST00000373296.8 | NP_001103348.1 | ||
TBX22 | NM_001109879.2 | c.-358-205_-358-200dupCACACA | 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.-2-241_-2-240insACACAC | intron_variant | Intron 1 of 8 | 5 | NM_001109878.2 | ENSP00000362393.3 | |||
TBX22 | ENST00000476373.1 | n.120-241_120-240insACACAC | intron_variant | Intron 1 of 1 | 3 | |||||
TBX22 | ENST00000626498.2 | n.-2-241_-2-240insACACAC | intron_variant | Intron 1 of 8 | 2 | ENSP00000487527.1 |
Frequencies
GnomAD3 genomes AF: 0.0163 AC: 1515AN: 92928Hom.: 21 Cov.: 0 AF XY: 0.0127 AC XY: 254AN XY: 20062
GnomAD3 genomes
AF:
AC:
1515
AN:
92928
Hom.:
Cov.:
0
AF XY:
AC XY:
254
AN XY:
20062
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0163 AC: 1515AN: 92946Hom.: 21 Cov.: 0 AF XY: 0.0127 AC XY: 256AN XY: 20090
GnomAD4 genome
AF:
AC:
1515
AN:
92946
Hom.:
Cov.:
0
AF XY:
AC XY:
256
AN XY:
20090
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at