3-196306938-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_152773.5(DYNLT2B):c.317+5G>A variant causes a splice region, intron change. The variant allele was found at a frequency of 0.00000806 in 1,612,312 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152773.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DYNLT2B | ENST00000325318.10 | c.317+5G>A | splice_region_variant, intron_variant | Intron 3 of 4 | 1 | NM_152773.5 | ENSP00000324323.5 | |||
ENSG00000272741 | ENST00000431391.1 | n.317+5G>A | splice_region_variant, intron_variant | Intron 3 of 5 | 5 | ENSP00000405181.1 | ||||
DYNLT2B | ENST00000426563.5 | n.*183+5G>A | splice_region_variant, intron_variant | Intron 3 of 4 | 2 | ENSP00000415835.1 | ||||
DYNLT2B | ENST00000446494.1 | n.317+5G>A | splice_region_variant, intron_variant | Intron 3 of 5 | 3 | ENSP00000410605.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152214Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251222Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135800
GnomAD4 exome AF: 0.00000822 AC: 12AN: 1460098Hom.: 0 Cov.: 29 AF XY: 0.00000826 AC XY: 6AN XY: 726552
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152214Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74360
ClinVar
Submissions by phenotype
DYNLT2B-related disorder Uncertain:1
The DYNLT2B c.317+5G>A variant is predicted to interfere with splicing. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0031% of alleles in individuals of European (Non-Finnish) descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
not provided Uncertain:1
This sequence change falls in intron 3 of the TCTEX1D2 gene. It does not directly change the encoded amino acid sequence of the TCTEX1D2 protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs201901599, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with TCTEX1D2-related conditions. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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