X-80022128-GGTTTTGTTTT-GGTTTTGTTTTGTTTT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

The NM_001109878.2(TBX22):​c.-2-119_-2-115dupGTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000223 in 552,501 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 34 hemizygotes in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00019 ( 0 hom., 4 hem., cov: 7)
Exomes 𝑓: 0.00023 ( 0 hom. 30 hem. )

Consequence

TBX22
NM_001109878.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.183
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000187 (20/106765) while in subpopulation EAS AF= 0.00122 (4/3276). AF 95% confidence interval is 0.000416. There are 0 homozygotes in gnomad4. There are 4 alleles in male gnomad4 subpopulation. Median coverage is 7. This position pass quality control queck.
BS2
High Hemizygotes in GnomAd4 at 4 XL gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TBX22NM_001109878.2 linkc.-2-119_-2-115dupGTTTT intron_variant Intron 1 of 8 ENST00000373296.8 NP_001103348.1 Q9Y458-1B3KUL8
TBX22NM_001109879.2 linkc.-358-119_-358-115dupGTTTT intron_variant Intron 1 of 8 NP_001103349.1 Q9Y458-2B3KUL8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TBX22ENST00000373296.8 linkc.-2-140_-2-139insGTTTT intron_variant Intron 1 of 8 5 NM_001109878.2 ENSP00000362393.3 Q9Y458-1
TBX22ENST00000476373.1 linkn.120-140_120-139insGTTTT intron_variant Intron 1 of 1 3
TBX22ENST00000626498.2 linkn.-2-140_-2-139insGTTTT intron_variant Intron 1 of 8 2 ENSP00000487527.1 A0A0D9SGI2

Frequencies

GnomAD3 genomes
AF:
0.000187
AC:
20
AN:
106765
Hom.:
0
Cov.:
7
AF XY:
0.000135
AC XY:
4
AN XY:
29543
show subpopulations
Gnomad AFR
AF:
0.0000341
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00122
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000385
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000231
Gnomad OTH
AF:
0.000696
GnomAD4 exome
AF:
0.000231
AC:
103
AN:
445736
Hom.:
0
AF XY:
0.000216
AC XY:
30
AN XY:
139198
show subpopulations
Gnomad4 AFR exome
AF:
0.000339
Gnomad4 AMR exome
AF:
0.000237
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000419
Gnomad4 SAS exome
AF:
0.000158
Gnomad4 FIN exome
AF:
0.0000879
Gnomad4 NFE exome
AF:
0.000238
Gnomad4 OTH exome
AF:
0.000596
GnomAD4 genome
AF:
0.000187
AC:
20
AN:
106765
Hom.:
0
Cov.:
7
AF XY:
0.000135
AC XY:
4
AN XY:
29543
show subpopulations
Gnomad4 AFR
AF:
0.0000341
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00122
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000385
Gnomad4 NFE
AF:
0.000231
Gnomad4 OTH
AF:
0.000696

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3048712; hg19: chrX-79277627; API