X-9684109-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_005647.4(TBL1X):c.278C>T(p.Thr93Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000827 in 1,209,681 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005647.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TBL1X | NM_005647.4 | c.278C>T | p.Thr93Met | missense_variant | Exon 6 of 18 | ENST00000645353.2 | NP_005638.1 | |
TBL1X | NM_001139466.1 | c.278C>T | p.Thr93Met | missense_variant | Exon 6 of 18 | NP_001132938.1 | ||
TBL1X | NM_001139467.1 | c.125C>T | p.Thr42Met | missense_variant | Exon 5 of 17 | NP_001132939.1 | ||
TBL1X | NM_001139468.1 | c.125C>T | p.Thr42Met | missense_variant | Exon 6 of 18 | NP_001132940.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000897 AC: 1AN: 111468Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33676
GnomAD3 exomes AF: 0.0000218 AC: 4AN: 183502Hom.: 0 AF XY: 0.0000442 AC XY: 3AN XY: 67932
GnomAD4 exome AF: 0.00000820 AC: 9AN: 1098213Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 3AN XY: 363569
GnomAD4 genome AF: 0.00000897 AC: 1AN: 111468Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33676
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.278C>T (p.T93M) alteration is located in exon 6 (coding exon 3) of the TBL1X gene. This alteration results from a C to T substitution at nucleotide position 278, causing the threonine (T) at amino acid position 93 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at