chrX-9688214-A-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_005647.4(TBL1X):āc.555A>Cā(p.Gln185His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000644 in 1,086,125 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. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_005647.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBL1X | NM_005647.4 | c.555A>C | p.Gln185His | missense_variant | 7/18 | ENST00000645353.2 | |
TBL1X | NM_001139466.1 | c.555A>C | p.Gln185His | missense_variant | 7/18 | ||
TBL1X | NM_001139467.1 | c.402A>C | p.Gln134His | missense_variant | 6/17 | ||
TBL1X | NM_001139468.1 | c.402A>C | p.Gln134His | missense_variant | 7/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBL1X | ENST00000645353.2 | c.555A>C | p.Gln185His | missense_variant | 7/18 | NM_005647.4 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD3 exomes AF: 0.0000257 AC: 4AN: 155515Hom.: 0 AF XY: 0.0000209 AC XY: 1AN XY: 47817
GnomAD4 exome AF: 0.00000644 AC: 7AN: 1086125Hom.: 0 Cov.: 32 AF XY: 0.00000847 AC XY: 3AN XY: 354279
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 03, 2021 | The c.555A>C (p.Q185H) alteration is located in exon 7 (coding exon 4) of the TBL1X gene. This alteration results from a A to C substitution at nucleotide position 555, causing the glutamine (Q) at amino acid position 185 to be replaced by a histidine (H). 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