15-66294996-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001143688.3(DIS3L):āc.148C>Gā(p.Leu50Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000292 in 1,611,498 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001143688.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DIS3L | NM_001143688.3 | c.148C>G | p.Leu50Val | missense_variant | 2/17 | ENST00000319212.9 | NP_001137160.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DIS3L | ENST00000319212.9 | c.148C>G | p.Leu50Val | missense_variant | 2/17 | 5 | NM_001143688.3 | ENSP00000321711 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152152Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000730 AC: 18AN: 246438Hom.: 0 AF XY: 0.0000450 AC XY: 6AN XY: 133364
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1459346Hom.: 0 Cov.: 30 AF XY: 0.0000248 AC XY: 18AN XY: 725866
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152152Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 08, 2023 | The c.148C>G (p.L50V) alteration is located in exon 2 (coding exon 2) of the DIS3L gene. This alteration results from a C to G substitution at nucleotide position 148, causing the leucine (L) at amino acid position 50 to be replaced by a valine (V). 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