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

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 = 0.000441 (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
TBX22NM_001109878.2 linkc.-2-211_-2-200delCACACACACACA intron_variant Intron 1 of 8 ENST00000373296.8 NP_001103348.1 Q9Y458-1B3KUL8
TBX22NM_001109879.2 linkc.-358-211_-358-200delCACACACACACA 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_-2-229delACACACACACAC intron_variant Intron 1 of 8 5 NM_001109878.2 ENSP00000362393.3 Q9Y458-1
TBX22ENST00000476373.1 linkn.120-240_120-229delACACACACACAC intron_variant Intron 1 of 1 3
TBX22ENST00000626498.2 linkn.-2-240_-2-229delACACACACACAC intron_variant Intron 1 of 8 2 ENSP00000487527.1 A0A0D9SGI2

Frequencies

GnomAD3 genomes
AF:
0.000430
AC:
40
AN:
92946
Hom.:
0
Cov.:
0
AF XY:
0.000349
AC XY:
7
AN XY:
20070
show subpopulations
Gnomad AFR
AF:
0.000773
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000118
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000337
Gnomad SAS
AF:
0.000547
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000374
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.000441
AC:
41
AN:
92964
Hom.:
0
Cov.:
0
AF XY:
0.000348
AC XY:
7
AN XY:
20098
show subpopulations
Gnomad4 AFR
AF:
0.000810
Gnomad4 AMR
AF:
0.000118
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000338
Gnomad4 SAS
AF:
0.000551
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000374
Gnomad4 OTH
AF:
0.00

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