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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.750
Variant links:
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
TBX22NM_001109878.2 linkc.-2-213_-2-200delCACACACACACACA intron_variant Intron 1 of 8 ENST00000373296.8 NP_001103348.1 Q9Y458-1B3KUL8
TBX22NM_001109879.2 linkc.-358-213_-358-200delCACACACACACACA intron_variant Intron 1 of 8 NP_001103349.1 Q9Y458-2B3KUL8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TBX22ENST00000373296.8 linkc.-2-240_-2-227delACACACACACACAC intron_variant Intron 1 of 8 5 NM_001109878.2 ENSP00000362393.3 Q9Y458-1
TBX22ENST00000476373.1 linkn.120-240_120-227delACACACACACACAC intron_variant Intron 1 of 1 3
TBX22ENST00000626498.2 linkn.-2-240_-2-227delACACACACACACAC intron_variant Intron 1 of 8 2 ENSP00000487527.1 A0A0D9SGI2

Frequencies

GnomAD3 genomes
AF:
0.00515
AC:
479
AN:
92944
Hom.:
2
Cov.:
0
AF XY:
0.00543
AC XY:
109
AN XY:
20068
show subpopulations
Gnomad AFR
AF:
0.0172
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00165
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000337
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000252
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000330
Gnomad OTH
AF:
0.00322
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.00516
AC:
480
AN:
92961
Hom.:
2
Cov.:
0
AF XY:
0.00547
AC XY:
110
AN XY:
20095
show subpopulations
Gnomad4 AFR
AF:
0.0172
Gnomad4 AMR
AF:
0.00165
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000338
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000252
Gnomad4 NFE
AF:
0.000330
Gnomad4 OTH
AF:
0.00318

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs200577659; hg19: chrX-79277526; API