chr6-166158524-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001366285.2(TBXT):c.1102G>A(p.Val368Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00223 in 1,603,094 control chromosomes in the GnomAD database, including 82 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V368L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001366285.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBXT | NM_001366285.2 | c.1102G>A | p.Val368Met | missense_variant | 8/8 | ENST00000366876.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBXT | ENST00000366876.7 | c.1102G>A | p.Val368Met | missense_variant | 8/8 | 1 | NM_001366285.2 | P4 | |
TBXT | ENST00000366871.7 | c.925G>A | p.Val309Met | missense_variant | 8/8 | 1 | |||
TBXT | ENST00000296946.6 | c.1099G>A | p.Val367Met | missense_variant | 9/9 | 5 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0116 AC: 1765AN: 152218Hom.: 45 Cov.: 33
GnomAD3 exomes AF: 0.00293 AC: 711AN: 242766Hom.: 14 AF XY: 0.00219 AC XY: 289AN XY: 132088
GnomAD4 exome AF: 0.00125 AC: 1807AN: 1450758Hom.: 37 Cov.: 34 AF XY: 0.00109 AC XY: 781AN XY: 719468
GnomAD4 genome AF: 0.0116 AC: 1766AN: 152336Hom.: 45 Cov.: 33 AF XY: 0.0111 AC XY: 826AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at