chrX-80023051-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001109878.2(TBX22):c.176-9G>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000108 in 1,208,287 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 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 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBX22 | NM_001109878.2 | c.176-9G>A | splice_polypyrimidine_tract_variant, intron_variant | ENST00000373296.8 | |||
TBX22 | NM_001109879.2 | c.-181-9G>A | splice_polypyrimidine_tract_variant, intron_variant | ||||
TBX22 | NM_016954.2 | c.176-9G>A | splice_polypyrimidine_tract_variant, intron_variant | ||||
TBX22 | NM_001303475.1 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBX22 | ENST00000373296.8 | c.176-9G>A | splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001109878.2 | P1 | |||
TBX22 | ENST00000373294.8 | c.176-9G>A | splice_polypyrimidine_tract_variant, intron_variant | 1 | P1 | ||||
TBX22 | ENST00000626498.2 | c.176-9G>A | splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | 2 | |||||
TBX22 | ENST00000626877.1 | upstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000180 AC: 2AN: 111267Hom.: 0 Cov.: 22 AF XY: 0.0000299 AC XY: 1AN XY: 33443
GnomAD3 exomes AF: 0.00000551 AC: 1AN: 181648Hom.: 0 AF XY: 0.0000151 AC XY: 1AN XY: 66234
GnomAD4 exome AF: 0.0000100 AC: 11AN: 1097020Hom.: 0 Cov.: 31 AF XY: 0.0000166 AC XY: 6AN XY: 362444
GnomAD4 genome ? AF: 0.0000180 AC: 2AN: 111267Hom.: 0 Cov.: 22 AF XY: 0.0000299 AC XY: 1AN XY: 33443
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 29, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at