Genetic Variant TBX22:c.-2-221_-2-200delCACACACACACACACACACACA (chrX-80022027-TACACACACACACACACACACAC-T) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001109878.2(TBX22):c.-2-221_-2-200delCACACACACACACACACACACA 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 0.000022 ( 0 hom., 0 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]

TBX22 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
TBX22	NM_001109878.2 link	c.-2-221_-2-200delCACACACACACACACACACACA	intron_variant	Intron 1 of 8	ENST00000373296.8	NP_001103348.1	Q9Y458-1B3KUL8
TBX22	NM_001109879.2 link	c.-358-221_-358-200delCACACACACACACACACACACA	intron_variant	Intron 1 of 8		NP_001103349.1	Q9Y458-2B3KUL8
TBX22	NM_016954.2 link	c.-242_-221delACACACACACACACACACACAC	upstream_gene_variant			NP_058650.1	Q9Y458-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
TBX22	ENST00000373296.8 link	c.-2-240_-2-219delACACACACACACACACACACAC	intron_variant	Intron 1 of 8	5	NM_001109878.2	ENSP00000362393.3	Q9Y458-1
TBX22	ENST00000476373.1 link	n.120-240_120-219delACACACACACACACACACACAC	intron_variant	Intron 1 of 1	3
TBX22	ENST00000626498.2 link	n.-2-240_-2-219delACACACACACACACACACACAC	intron_variant	Intron 1 of 8	2		ENSP00000487527.1	A0A0D9SGI2
TBX22	ENST00000373294.8 link	c.-242_-221delACACACACACACACACACACAC	upstream_gene_variant		1		ENSP00000362390.5	Q9Y458-1

Frequencies

GnomAD3 genomes

AF:

0.0000215

AC:

AN:

92946

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

20070

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000252

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000220

Gnomad OTH

AF:

0.00

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0000215

AC:

AN:

92946

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

20070

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000252

Gnomad4 NFE

AF:

0.0000220

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over