X-80022341-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001109878.2(TBX22):c.72C>T(p.Leu24Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00176 in 1,209,470 control chromosomes in the GnomAD database, including 22 homozygotes. There are 545 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 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TBX22 | NM_001109878.2 | c.72C>T | p.Leu24Leu | synonymous_variant | Exon 2 of 9 | ENST00000373296.8 | NP_001103348.1 | |
TBX22 | NM_016954.2 | c.72C>T | p.Leu24Leu | synonymous_variant | Exon 1 of 8 | NP_058650.1 | ||
TBX22 | NM_001109879.2 | c.-285C>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.72C>T | p.Leu24Leu | synonymous_variant | Exon 2 of 9 | 5 | NM_001109878.2 | ENSP00000362393.3 | ||
TBX22 | ENST00000373294.8 | c.72C>T | p.Leu24Leu | synonymous_variant | Exon 1 of 8 | 1 | ENSP00000362390.5 | |||
TBX22 | ENST00000476373.1 | n.193C>T | non_coding_transcript_exon_variant | Exon 2 of 2 | 3 | |||||
TBX22 | ENST00000626498.2 | n.72C>T | non_coding_transcript_exon_variant | Exon 2 of 9 | 2 | ENSP00000487527.1 |
Frequencies
GnomAD3 genomes AF: 0.00792 AC: 883AN: 111547Hom.: 10 Cov.: 22 AF XY: 0.00634 AC XY: 214AN XY: 33769
GnomAD3 exomes AF: 0.00297 AC: 543AN: 182765Hom.: 8 AF XY: 0.00202 AC XY: 136AN XY: 67285
GnomAD4 exome AF: 0.00112 AC: 1230AN: 1097873Hom.: 12 Cov.: 31 AF XY: 0.000886 AC XY: 322AN XY: 363239
GnomAD4 genome AF: 0.00803 AC: 896AN: 111597Hom.: 10 Cov.: 22 AF XY: 0.00659 AC XY: 223AN XY: 33829
ClinVar
Submissions by phenotype
not provided Benign:2
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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