X-9688157-T-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_005647.4(TBL1X):āc.498T>Gā(p.Ala166Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000785 in 1,195,525 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 265 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_005647.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TBL1X | NM_005647.4 | c.498T>G | p.Ala166Ala | synonymous_variant | Exon 7 of 18 | ENST00000645353.2 | NP_005638.1 | |
TBL1X | NM_001139466.1 | c.498T>G | p.Ala166Ala | synonymous_variant | Exon 7 of 18 | NP_001132938.1 | ||
TBL1X | NM_001139467.1 | c.345T>G | p.Ala115Ala | synonymous_variant | Exon 6 of 17 | NP_001132939.1 | ||
TBL1X | NM_001139468.1 | c.345T>G | p.Ala115Ala | synonymous_variant | Exon 7 of 18 | NP_001132940.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000562 AC: 63AN: 112022Hom.: 0 Cov.: 24 AF XY: 0.000409 AC XY: 14AN XY: 34224
GnomAD3 exomes AF: 0.000435 AC: 65AN: 149516Hom.: 1 AF XY: 0.000549 AC XY: 26AN XY: 47328
GnomAD4 exome AF: 0.000808 AC: 876AN: 1083503Hom.: 0 Cov.: 32 AF XY: 0.000711 AC XY: 251AN XY: 353245
GnomAD4 genome AF: 0.000562 AC: 63AN: 112022Hom.: 0 Cov.: 24 AF XY: 0.000409 AC XY: 14AN XY: 34224
ClinVar
Submissions by phenotype
not provided Benign:1
TBL1X: BP4, BP7 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at