3-196306977-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_152773.5(DYNLT2B):āc.283G>Cā(p.Val95Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000291 in 1,614,118 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_152773.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DYNLT2B | ENST00000325318.10 | c.283G>C | p.Val95Leu | missense_variant | Exon 3 of 5 | 1 | NM_152773.5 | ENSP00000324323.5 | ||
ENSG00000272741 | ENST00000431391.1 | n.283G>C | non_coding_transcript_exon_variant | Exon 3 of 6 | 5 | ENSP00000405181.1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251348Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135852
GnomAD4 exome AF: 0.0000246 AC: 36AN: 1461814Hom.: 0 Cov.: 30 AF XY: 0.0000289 AC XY: 21AN XY: 727214
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152304Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74474
ClinVar
Submissions by phenotype
not provided Uncertain:1
This variant has not been reported in the literature in individuals affected with TCTEX1D2-related conditions. This sequence change replaces valine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 95 of the TCTEX1D2 protein (p.Val95Leu). This variant is present in population databases (rs139637513, gnomAD 0.02%). ClinVar contains an entry for this variant (Variation ID: 1909989). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at