NM_001109878.2:c.176-13C>A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001109878.2(TBX22):c.176-13C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00628 in 1,208,342 control chromosomes in the GnomAD database, including 24 homozygotes. There are 2,345 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001109878.2 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TBX22 | NM_001109878.2 | c.176-13C>A | intron_variant | Intron 2 of 8 | ENST00000373296.8 | NP_001103348.1 | ||
TBX22 | NM_016954.2 | c.176-13C>A | intron_variant | Intron 1 of 7 | NP_058650.1 | |||
TBX22 | NM_001109879.2 | c.-181-13C>A | intron_variant | Intron 2 of 8 | NP_001103349.1 | |||
TBX22 | NM_001303475.1 | c.-261C>A | upstream_gene_variant | NP_001290404.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TBX22 | ENST00000373296.8 | c.176-13C>A | intron_variant | Intron 2 of 8 | 5 | NM_001109878.2 | ENSP00000362393.3 | |||
TBX22 | ENST00000373294.8 | c.176-13C>A | intron_variant | Intron 1 of 7 | 1 | ENSP00000362390.5 | ||||
TBX22 | ENST00000626498.2 | n.176-13C>A | intron_variant | Intron 2 of 8 | 2 | ENSP00000487527.1 | ||||
TBX22 | ENST00000626877.1 | n.-22C>A | upstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.00441 AC: 490AN: 111175Hom.: 0 Cov.: 22 AF XY: 0.00417 AC XY: 139AN XY: 33349
GnomAD3 exomes AF: 0.00445 AC: 807AN: 181147Hom.: 2 AF XY: 0.00437 AC XY: 287AN XY: 65747
GnomAD4 exome AF: 0.00647 AC: 7100AN: 1097114Hom.: 24 Cov.: 31 AF XY: 0.00608 AC XY: 2206AN XY: 362558
GnomAD4 genome AF: 0.00440 AC: 489AN: 111228Hom.: 0 Cov.: 22 AF XY: 0.00416 AC XY: 139AN XY: 33412
ClinVar
Submissions by phenotype
Cleft palate with or without ankyloglossia, X-linked Benign:2
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
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not provided Benign:2
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TBX22: BS1 -
TBX22-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at