3-196296055-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_152773.5(DYNLT2B):c.332G>A(p.Cys111Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.0000136 in 1,613,728 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152773.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DYNLT2B | ENST00000325318.10 | c.332G>A | p.Cys111Tyr | missense_variant | Exon 4 of 5 | 1 | NM_152773.5 | ENSP00000324323.5 | ||
ENSG00000272741 | ENST00000431391.1 | n.317+10888G>A | intron_variant | Intron 3 of 5 | 5 | ENSP00000405181.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152152Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251260Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135802
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461576Hom.: 0 Cov.: 30 AF XY: 0.00000825 AC XY: 6AN XY: 727074
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152152Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.332G>A (p.C111Y) alteration is located in exon 4 (coding exon 4) of the TCTEX1D2 gene. This alteration results from a G to A substitution at nucleotide position 332, causing the cysteine (C) at amino acid position 111 to be replaced by a tyrosine (Y). 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