X-9688157-T-TGCGGCC
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3BS2
The NM_005647.4(TBL1X):c.499_504dupGCGGCC(p.Ala167_Ala168dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000212 in 1,083,556 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005647.4 conservative_inframe_insertion
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.499_504dupGCGGCC | p.Ala167_Ala168dup | conservative_inframe_insertion | Exon 7 of 18 | ENST00000645353.2 | NP_005638.1 | |
TBL1X | NM_001139466.1 | c.499_504dupGCGGCC | p.Ala167_Ala168dup | conservative_inframe_insertion | Exon 7 of 18 | NP_001132938.1 | ||
TBL1X | NM_001139467.1 | c.346_351dupGCGGCC | p.Ala116_Ala117dup | conservative_inframe_insertion | Exon 6 of 17 | NP_001132939.1 | ||
TBL1X | NM_001139468.1 | c.346_351dupGCGGCC | p.Ala116_Ala117dup | conservative_inframe_insertion | Exon 7 of 18 | NP_001132940.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 24
GnomAD4 exome AF: 0.0000212 AC: 23AN: 1083556Hom.: 0 Cov.: 32 AF XY: 0.0000142 AC XY: 5AN XY: 353298
GnomAD4 genome Cov.: 24
ClinVar
Submissions by phenotype
not provided Uncertain:1
In-frame insertion of 2 amino acids in a repetitive region with no known function; Not observed at significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at