X-80022027-T-TAC

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

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

• Frequency: Genomes: 𝑓 0.13 (707 hom., 2267 hem., cov: 0)
• Consequence: TBX22 NM_001109878.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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 -10 ACMG points.

• BP6: Variant X-80022027-T-TAC is Benign according to our data. Variant chrX-80022027-T-TAC is described in ClinVar as [Benign]. Clinvar id is 1291809.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TBX22	NM_001109878.2	c.-2-201_-2-200dup		intron_variant		ENST00000373296.8
TBX22	NM_001109879.2	c.-358-201_-358-200dup		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TBX22	ENST00000373296.8	c.-2-201_-2-200dup		intron_variant		5	NM_001109878.2	P1
TBX22	ENST00000626498.2	c.-2-201_-2-200dup		intron_variant, NMD_transcript_variant		2
TBX22	ENST00000476373.1	n.120-201_120-200dup		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.135 AC: 12479 AN: 92762 Hom.: 706 Cov.: 0 AF XY: 0.113 AC XY: 2261 AN XY: 19970

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.0882

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0600

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.135 AC: 12483 AN: 92778 Hom.: 707 Cov.: 0 AF XY: 0.113 AC XY: 2267 AN XY: 19998

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.0882

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.0598

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.132

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 20, 2021

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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;