X-80022027-TACACACACACACACACACACAC-TACACACAC

Variant names:

• chrX-80022027-TACACACACACACAC-T
• rs200577659
• NM_001109878.2:c.-2-213_-2-200delCACACACACACACA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

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
• 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]

ACMG classification

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
TBX22	NM_001109878.2	c.-2-213_-2-200delCACACACACACACA		intron_variant	Intron 1 of 8	ENST00000373296.8	NP_001103348.1
TBX22	NM_001109879.2	c.-358-213_-358-200delCACACACACACACA		intron_variant	Intron 1 of 8		NP_001103349.1
TBX22	NM_016954.2	c.-242_-229delACACACACACACAC		upstream_gene_variant			NP_058650.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TBX22	ENST00000373296.8	c.-2-240_-2-227delACACACACACACAC		intron_variant	Intron 1 of 8	5	NM_001109878.2	ENSP00000362393.3
TBX22	ENST00000476373.1	n.120-240_120-227delACACACACACACAC		intron_variant	Intron 1 of 1	3
TBX22	ENST00000626498.2	n.-2-240_-2-227delACACACACACACAC		intron_variant	Intron 1 of 8	2		ENSP00000487527.1
TBX22	ENST00000373294.8	c.-242_-229delACACACACACACAC		upstream_gene_variant		1		ENSP00000362390.5

Frequencies

GnomAD3 genomes AF: 0.00515 AC: 479 AN: 92944 Hom.: 2 Cov.: 0 AF XY: 0.00543 AC XY: 109 AN XY: 20068

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

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs200577659; hg19: chrX-79277526;