rs1156605251
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM1PP3
The NM_001109878.2(TBX22):c.448A>C(p.Lys150Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000911 in 1,207,301 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. 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 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBX22 | NM_001109878.2 | c.448A>C | p.Lys150Gln | missense_variant | 4/9 | ENST00000373296.8 | |
TBX22 | NM_016954.2 | c.448A>C | p.Lys150Gln | missense_variant | 3/8 | ||
TBX22 | NM_001109879.2 | c.88A>C | p.Lys30Gln | missense_variant | 4/9 | ||
TBX22 | NM_001303475.1 | c.88A>C | p.Lys30Gln | missense_variant | 2/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBX22 | ENST00000373296.8 | c.448A>C | p.Lys150Gln | missense_variant | 4/9 | 5 | NM_001109878.2 | P1 | |
TBX22 | ENST00000373294.8 | c.448A>C | p.Lys150Gln | missense_variant | 3/8 | 1 | P1 | ||
TBX22 | ENST00000626877.1 | n.327A>C | non_coding_transcript_exon_variant | 2/7 | 1 | ||||
TBX22 | ENST00000626498.2 | c.*60A>C | 3_prime_UTR_variant, NMD_transcript_variant | 4/9 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000180 AC: 2AN: 110948Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33148
GnomAD3 exomes AF: 0.0000109 AC: 2AN: 183376Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67816
GnomAD4 exome AF: 0.00000821 AC: 9AN: 1096353Hom.: 0 Cov.: 30 AF XY: 0.00000829 AC XY: 3AN XY: 361737
GnomAD4 genome ? AF: 0.0000180 AC: 2AN: 110948Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33148
ClinVar
Submissions by phenotype
Cleft palate;C3266076:Orofacial cleft Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Jan 01, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at