X-80014787-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001109878.2(TBX22):c.-103G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0226 in 112,233 control chromosomes in the GnomAD database, including 68 homozygotes. There are 660 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001109878.2 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TBX22 | ENST00000373296 | c.-103G>A | 5_prime_UTR_variant | Exon 1 of 9 | 5 | NM_001109878.2 | ENSP00000362393.3 | |||
TBX22 | ENST00000476373.1 | n.19G>A | non_coding_transcript_exon_variant | Exon 1 of 2 | 3 | |||||
TBX22 | ENST00000626498.2 | n.-103G>A | non_coding_transcript_exon_variant | Exon 1 of 9 | 2 | ENSP00000487527.1 | ||||
TBX22 | ENST00000626498.2 | n.-103G>A | 5_prime_UTR_variant | Exon 1 of 9 | 2 | ENSP00000487527.1 |
Frequencies
GnomAD3 genomes AF: 0.0225 AC: 2525AN: 112182Hom.: 68 Cov.: 22 AF XY: 0.0191 AC XY: 657AN XY: 34350
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 54Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 34
GnomAD4 genome AF: 0.0226 AC: 2531AN: 112233Hom.: 68 Cov.: 22 AF XY: 0.0192 AC XY: 660AN XY: 34411
ClinVar
Submissions by phenotype
Cleft palate with or without ankyloglossia, X-linked Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at