X-80022027-T-TACAC

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_001109878.2(TBX22):c.-2-203_-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 0.11 (614 hom., 2035 hem., cov: 0)
  • Failed GnomAD Quality Control
• 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 Likely_benign. Variant got -6 ACMG points.

• BP6: Variant X-80022027-T-TACAC is Benign according to our data. Variant chrX-80022027-T-TACAC is described in ClinVar as [Benign]. Clinvar id is 1297948.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd at 615 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TBX22	NM_001109878.2	c.-2-203_-2-200dup		intron_variant		ENST00000373296.8
TBX22	NM_001109879.2	c.-358-203_-358-200dup		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TBX22	ENST00000373296.8	c.-2-203_-2-200dup		intron_variant		5	NM_001109878.2	P1
TBX22	ENST00000626498.2	c.-2-203_-2-200dup		intron_variant, NMD_transcript_variant		2
TBX22	ENST00000476373.1	n.120-203_120-200dup		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.114 AC: 10608 AN: 92820 Hom.: 615 Cov.: 0 AF XY: 0.101 AC XY: 2030 AN XY: 20026

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.0878

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.0892

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.0737

Gnomad FIN AF: 0.0702

Gnomad MID AF: 0.0505

Gnomad NFE AF: 0.0957

Gnomad OTH AF: 0.147

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.114 AC: 10611 AN: 92838 Hom.: 614 Cov.: 0 AF XY: 0.101 AC XY: 2035 AN XY: 20054

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.0892

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.0738

Gnomad4 FIN AF: 0.0702

Gnomad4 NFE AF: 0.0956

Gnomad4 OTH AF: 0.148

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 19, 2021

- -

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;