rs3048712
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001109878.2(TBX22):c.-2-124_-2-115delGTTTTGTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000163 in 552,496 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000094 ( 0 hom., 0 hem., cov: 6)
Exomes 𝑓: 0.000018 ( 0 hom. 5 hem. )
Consequence
TBX22
NM_001109878.2 intron
NM_001109878.2 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.726
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High Hemizygotes in GnomAdExome4 at 5 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TBX22 | NM_001109878.2 | c.-2-124_-2-115delGTTTTGTTTT | intron_variant | Intron 1 of 8 | ENST00000373296.8 | NP_001103348.1 | ||
TBX22 | NM_001109879.2 | c.-358-124_-358-115delGTTTTGTTTT | intron_variant | Intron 1 of 8 | NP_001103349.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TBX22 | ENST00000373296.8 | c.-2-139_-2-130delGTTTTGTTTT | intron_variant | Intron 1 of 8 | 5 | NM_001109878.2 | ENSP00000362393.3 | |||
TBX22 | ENST00000476373.1 | n.120-139_120-130delGTTTTGTTTT | intron_variant | Intron 1 of 1 | 3 | |||||
TBX22 | ENST00000626498.2 | n.-2-139_-2-130delGTTTTGTTTT | intron_variant | Intron 1 of 8 | 2 | ENSP00000487527.1 |
Frequencies
GnomAD3 genomes AF: 0.00000937 AC: 1AN: 106765Hom.: 0 Cov.: 6 AF XY: 0.00 AC XY: 0AN XY: 29543
GnomAD3 genomes
AF:
AC:
1
AN:
106765
Hom.:
Cov.:
6
AF XY:
AC XY:
0
AN XY:
29543
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0000179 AC: 8AN: 445687Hom.: 0 AF XY: 0.0000359 AC XY: 5AN XY: 139163
GnomAD4 exome
AF:
AC:
8
AN:
445687
Hom.:
AF XY:
AC XY:
5
AN XY:
139163
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.00000936 AC: 1AN: 106809Hom.: 0 Cov.: 6 AF XY: 0.00 AC XY: 0AN XY: 29599
GnomAD4 genome
AF:
AC:
1
AN:
106809
Hom.:
Cov.:
6
AF XY:
AC XY:
0
AN XY:
29599
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at