X-80022027-TACACACACACACACACACACAC-TACACACACACACACACACAC

Variant names:

• chrX-80022027-TAC-T
• rs200577659
• NM_001109878.2:c.-2-201_-2-200delCA

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001109878.2(TBX22):​c.-2-201_-2-200delCA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.082 (300 hom., 1481 hem., cov: 0)
• Consequence: TBX22 NM_001109878.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.750
• Publications: 1 publications found

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 Gene-Disease associations (from GenCC):

• cleft palate with or without ankyloglossia, X-linked

  Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, ClinGen, G2P, PanelApp Australia, Labcorp Genetics (formerly Invitae)
• Abruzzo-Erickson syndrome

  Inheritance: XL Classification: SUPPORTIVE, LIMITED Submitted by: Orphanet, G2P

ENSG00000300464 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant X-80022027-TAC-T is Benign according to our data. Variant chrX-80022027-TAC-T is described in ClinVar as Benign. ClinVar VariationId is 1224711.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001109878.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TBX22	NM_001109878.2	MANE Select	c.-2-201_-2-200delCA		intron	N/A	NP_001103348.1	Q9Y458-1
	TBX22	NM_001109879.2		c.-358-201_-358-200delCA		intron	N/A	NP_001103349.1	Q9Y458-2
	TBX22	NM_016954.2		c.-242_-241delAC		upstream_gene	N/A	NP_058650.1	Q9Y458-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TBX22	ENST00000373296.8	TSL:5 MANE Select	c.-2-240_-2-239delAC		intron	N/A	ENSP00000362393.3	Q9Y458-1
	TBX22	ENST00000968708.1		c.-3+154_-3+155delAC		intron	N/A	ENSP00000638767.1
	TBX22	ENST00000476373.1	TSL:3	n.120-240_120-239delAC		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0821 AC: 7614 AN: 92744 Hom.: 300 Cov.: 0

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.0189

Gnomad AMR AF: 0.0633

Gnomad ASJ AF: 0.0527

Gnomad EAS AF: 0.0505

Gnomad SAS AF: 0.0601

Gnomad FIN AF: 0.0458

Gnomad MID AF: 0.0711

Gnomad NFE AF: 0.0550

Gnomad OTH AF: 0.0823

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

GnomAD4 genome AF: 0.0822 AC: 7624 AN: 92760 Hom.: 300 Cov.: 0 AF XY: 0.0741 AC XY: 1481 AN XY: 19994

African (AFR) AF: 0.151 AC: 3903 AN: 25867

American (AMR) AF: 0.0638 AC: 542 AN: 8492

Ashkenazi Jewish (ASJ) AF: 0.0527 AC: 120 AN: 2275

East Asian (EAS) AF: 0.0510 AC: 151 AN: 2961

South Asian (SAS) AF: 0.0579 AC: 105 AN: 1815

European-Finnish (FIN) AF: 0.0458 AC: 180 AN: 3929

Middle Eastern (MID) AF: 0.0791 AC: 14 AN: 177

European-Non Finnish (NFE) AF: 0.0550 AC: 2496 AN: 45406

Other (OTH) AF: 0.0811 AC: 102 AN: 1257

Alfa AF: 0.0189 Hom.: 192

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.75
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs200577659; hg19: chrX-79277526; COSMIC: COSV64787341; COSMIC: COSV64787341;