X-80022322-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001109878.2(TBX22):c.53G>T(p.Arg18Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000899 in 111,260 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001109878.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TBX22 | NM_001109878.2 | c.53G>T | p.Arg18Ile | missense_variant | Exon 2 of 9 | ENST00000373296.8 | NP_001103348.1 | |
TBX22 | NM_016954.2 | c.53G>T | p.Arg18Ile | missense_variant | Exon 1 of 8 | NP_058650.1 | ||
TBX22 | NM_001109879.2 | c.-304G>T | 5_prime_UTR_variant | Exon 2 of 9 | NP_001103349.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TBX22 | ENST00000373296.8 | c.53G>T | p.Arg18Ile | missense_variant | Exon 2 of 9 | 5 | NM_001109878.2 | ENSP00000362393.3 | ||
TBX22 | ENST00000373294.8 | c.53G>T | p.Arg18Ile | missense_variant | Exon 1 of 8 | 1 | ENSP00000362390.5 | |||
TBX22 | ENST00000476373.1 | n.174G>T | non_coding_transcript_exon_variant | Exon 2 of 2 | 3 | |||||
TBX22 | ENST00000626498.2 | n.53G>T | non_coding_transcript_exon_variant | Exon 2 of 9 | 2 | ENSP00000487527.1 |
Frequencies
GnomAD3 genomes AF: 0.00000899 AC: 1AN: 111260Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33476
GnomAD4 exome Cov.: 31
GnomAD4 genome AF: 0.00000899 AC: 1AN: 111260Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33476
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.53G>T (p.R18I) alteration is located in exon 2 (coding exon 1) of the TBX22 gene. This alteration results from a G to T substitution at nucleotide position 53, causing the arginine (R) at amino acid position 18 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at