X-80022027-TACACACACACACACACACACAC-TACACACACACAC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

The NM_001109878.2(TBX22):​c.-2-209_-2-200delCACACACACA 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 0.0028 ( 0 hom., 65 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 eas. gnomad4 allele frequency = 0.00281 (261/92959) while in subpopulation EAS AF= 0.0115 (34/2959). AF 95% confidence interval is 0.00845. There are 0 homozygotes in gnomad4. There are 65 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High Hemizygotes in GnomAd4 at 65 XL gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TBX22NM_001109878.2 linkc.-2-209_-2-200delCACACACACA intron_variant Intron 1 of 8 ENST00000373296.8 NP_001103348.1 Q9Y458-1B3KUL8
TBX22NM_001109879.2 linkc.-358-209_-358-200delCACACACACA 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_-2-231delACACACACAC intron_variant Intron 1 of 8 5 NM_001109878.2 ENSP00000362393.3 Q9Y458-1
TBX22ENST00000476373.1 linkn.120-240_120-231delACACACACAC intron_variant Intron 1 of 1 3
TBX22ENST00000626498.2 linkn.-2-240_-2-231delACACACACAC intron_variant Intron 1 of 8 2 ENSP00000487527.1 A0A0D9SGI2

Frequencies

GnomAD3 genomes
AF:
0.00281
AC:
261
AN:
92941
Hom.:
0
Cov.:
0
AF XY:
0.00324
AC XY:
65
AN XY:
20067
show subpopulations
Gnomad AFR
AF:
0.00290
Gnomad AMI
AF:
0.00172
Gnomad AMR
AF:
0.00612
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.0115
Gnomad SAS
AF:
0.00109
Gnomad FIN
AF:
0.000505
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00196
Gnomad OTH
AF:
0.00483
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.00281
AC:
261
AN:
92959
Hom.:
0
Cov.:
0
AF XY:
0.00323
AC XY:
65
AN XY:
20095
show subpopulations
Gnomad4 AFR
AF:
0.00289
Gnomad4 AMR
AF:
0.00611
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.0115
Gnomad4 SAS
AF:
0.00110
Gnomad4 FIN
AF:
0.000505
Gnomad4 NFE
AF:
0.00196
Gnomad4 OTH
AF:
0.00477

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