X-9654237-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_005647.4(TBL1X):c.126C>T(p.Asn42Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000116 in 1,208,265 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 39 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_005647.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TBL1X | NM_005647.4 | c.126C>T | p.Asn42Asn | synonymous_variant | Exon 5 of 18 | ENST00000645353.2 | NP_005638.1 | |
TBL1X | NM_001139466.1 | c.126C>T | p.Asn42Asn | synonymous_variant | Exon 5 of 18 | NP_001132938.1 | ||
TBL1X | NM_001139467.1 | c.-28C>T | 5_prime_UTR_variant | Exon 4 of 17 | NP_001132939.1 | |||
TBL1X | NM_001139468.1 | c.-28C>T | 5_prime_UTR_variant | Exon 5 of 18 | NP_001132940.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000361 AC: 4AN: 110734Hom.: 0 Cov.: 23 AF XY: 0.0000303 AC XY: 1AN XY: 33008
GnomAD3 exomes AF: 0.000104 AC: 19AN: 183285Hom.: 0 AF XY: 0.000103 AC XY: 7AN XY: 67725
GnomAD4 exome AF: 0.000124 AC: 136AN: 1097531Hom.: 0 Cov.: 31 AF XY: 0.000105 AC XY: 38AN XY: 363017
GnomAD4 genome AF: 0.0000361 AC: 4AN: 110734Hom.: 0 Cov.: 23 AF XY: 0.0000303 AC XY: 1AN XY: 33008
ClinVar
Submissions by phenotype
TBL1X-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at