rs745307654
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PM4_Supporting
The NM_152383.5(DIS3L2):βc.2620_2622delβ(p.Glu874del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000213 in 1,456,852 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (β β ). Synonymous variant affecting the same amino acid position (i.e. K870K) has been classified as Likely benign.
Frequency
Consequence
NM_152383.5 inframe_deletion
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DIS3L2 | NM_152383.5 | c.2620_2622del | p.Glu874del | inframe_deletion | 21/21 | ENST00000325385.12 | |
DIS3L2 | NM_001257281.2 | c.1582-6753_1582-6751del | intron_variant | ||||
DIS3L2 | NR_046476.2 | n.2693_2695del | non_coding_transcript_exon_variant | 21/21 | |||
DIS3L2 | NR_046477.2 | n.3266_3268del | non_coding_transcript_exon_variant | 19/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DIS3L2 | ENST00000325385.12 | c.2620_2622del | p.Glu874del | inframe_deletion | 21/21 | 5 | NM_152383.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000411 AC: 1AN: 243444Hom.: 0 AF XY: 0.00000751 AC XY: 1AN XY: 133172
GnomAD4 exome AF: 0.0000213 AC: 31AN: 1456852Hom.: 0 AF XY: 0.0000248 AC XY: 18AN XY: 724950
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Perlman syndrome Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center | Mar 29, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 15, 2023 | This variant, c.2620_2622del, results in the deletion of 1 amino acid(s) of the DIS3L2 protein (p.Glu874del), but otherwise preserves the integrity of the reading frame. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with DIS3L2-related conditions. ClinVar contains an entry for this variant (Variation ID: 531955). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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