chr6-166158460-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001366285.2(TBXT):āc.1166A>Gā(p.His389Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,613,824 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001366285.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBXT | NM_001366285.2 | c.1166A>G | p.His389Arg | missense_variant | 8/8 | ENST00000366876.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBXT | ENST00000366876.7 | c.1166A>G | p.His389Arg | missense_variant | 8/8 | 1 | NM_001366285.2 | P4 | |
TBXT | ENST00000366871.7 | c.989A>G | p.His330Arg | missense_variant | 8/8 | 1 | |||
TBXT | ENST00000296946.6 | c.1163A>G | p.His388Arg | missense_variant | 9/9 | 5 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 152072Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250878Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135732
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461752Hom.: 0 Cov.: 33 AF XY: 0.00000413 AC XY: 3AN XY: 727194
GnomAD4 genome AF: 0.0000855 AC: 13AN: 152072Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74272
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2023 | The c.1163A>G (p.H388R) alteration is located in exon 9 (coding exon 8) of the T gene. This alteration results from a A to G substitution at nucleotide position 1163, causing the histidine (H) at amino acid position 388 to be replaced by an arginine (R). 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