2-232343480-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_ModeratePM2
The NM_001257281.2(DIS3L2):c.1717C>T(p.Arg573*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000148 in 1,555,772 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 (no stars).
Frequency
Consequence
NM_001257281.2 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152140Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000494 AC: 8AN: 161984Hom.: 0 AF XY: 0.0000349 AC XY: 3AN XY: 86038
GnomAD4 exome AF: 0.0000150 AC: 21AN: 1403632Hom.: 0 Cov.: 30 AF XY: 0.0000115 AC XY: 8AN XY: 692754
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152140Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74314
ClinVar
Submissions by phenotype
DIS3L2-related disorder Uncertain:1
The DIS3L2 c.1717C>T variant is predicted to result in premature protein termination (p.Arg573*). To our knowledge, this variant has not been reported in the literature. This variant is post coding on the main transcript NM_152383:c.*6850C>T and is not expected to impact protein function. This variant is reported in 0.031% of alleles in individuals of Latino descent in gnomAD. Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at