chrX-80022128-G-GGTTTTGTTTT

Variant names:

• chrX-80022128-G-GGTTTTGTTTT
• NM_001109878.2:c.-2-124_-2-115dupGTTTTGTTTT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001109878.2(TBX22):​c.-2-124_-2-115dupGTTTTGTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000224 in 445,737 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 7)
  • Exomes 𝑓: 0.0000022 (0 hom. 0 hem.)
• Consequence: TBX22 NM_001109878.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TBX22	NM_001109878.2	c.-2-124_-2-115dupGTTTTGTTTT		intron_variant	Intron 1 of 8	ENST00000373296.8	NP_001103348.1
TBX22	NM_001109879.2	c.-358-124_-358-115dupGTTTTGTTTT		intron_variant	Intron 1 of 8		NP_001103349.1
TBX22	NM_016954.2	c.-142_-141insGTTTTGTTTT		upstream_gene_variant			NP_058650.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TBX22	ENST00000373296.8	c.-2-140_-2-139insGTTTTGTTTT		intron_variant	Intron 1 of 8	5	NM_001109878.2	ENSP00000362393.3
TBX22	ENST00000476373.1	n.120-140_120-139insGTTTTGTTTT		intron_variant	Intron 1 of 1	3
TBX22	ENST00000626498.2	n.-2-140_-2-139insGTTTTGTTTT		intron_variant	Intron 1 of 8	2		ENSP00000487527.1
TBX22	ENST00000373294.8	c.-142_-141insGTTTTGTTTT		upstream_gene_variant		1		ENSP00000362390.5

Frequencies

GnomAD3 genomes Cov.: 7

GnomAD4 exome AF: 0.00000224 AC: 1 AN: 445737 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 139199

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000419

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 7

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

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-79277627;