rs148106618
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6BP7BS1
The NM_152383.5(DIS3L2):c.2409G>T(p.Arg803=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000139 in 1,550,542 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. R803R) has been classified as Likely benign.
Frequency
Consequence
NM_152383.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DIS3L2 | NM_152383.5 | c.2409G>T | p.Arg803= | synonymous_variant | 20/21 | ENST00000325385.12 | |
DIS3L2 | NM_001257281.2 | c.1582-7558G>T | intron_variant | ||||
DIS3L2 | NR_046476.2 | n.2482G>T | non_coding_transcript_exon_variant | 20/21 | |||
DIS3L2 | NR_046477.2 | n.2461G>T | non_coding_transcript_exon_variant | 19/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DIS3L2 | ENST00000325385.12 | c.2409G>T | p.Arg803= | synonymous_variant | 20/21 | 5 | NM_152383.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152244Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000156 AC: 24AN: 154316Hom.: 0 AF XY: 0.000183 AC XY: 15AN XY: 81752
GnomAD4 exome AF: 0.000139 AC: 194AN: 1398180Hom.: 0 Cov.: 30 AF XY: 0.000142 AC XY: 98AN XY: 689604
GnomAD4 genome AF: 0.000144 AC: 22AN: 152362Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74506
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jul 05, 2019 | Has not been previously published as pathogenic or benign to our knowledge; In silico analysis, which includes splice predictors and evolutionary conservation, suggests this variant may impact gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown. - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2024 | DIS3L2: BP4, BP7 - |
Perlman syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 04, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at