chr2-232334452-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_152383.5(DIS3L2):c.2242C>T(p.Arg748Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,613,958 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 Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R748G) has been classified as Uncertain significance.
Frequency
Consequence
NM_152383.5 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 | UniProt |
---|---|---|---|---|---|---|---|
DIS3L2 | NM_152383.5 | c.2242C>T | p.Arg748Cys | missense_variant | 18/21 | ENST00000325385.12 | |
DIS3L2 | NM_001257281.2 | c.1582-8893C>T | intron_variant | ||||
DIS3L2 | NR_046476.2 | n.2315C>T | non_coding_transcript_exon_variant | 18/21 | |||
DIS3L2 | NR_046477.2 | n.2294C>T | non_coding_transcript_exon_variant | 17/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DIS3L2 | ENST00000325385.12 | c.2242C>T | p.Arg748Cys | missense_variant | 18/21 | 5 | NM_152383.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152256Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000322 AC: 8AN: 248602Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135170
GnomAD4 exome AF: 0.0000349 AC: 51AN: 1461584Hom.: 0 Cov.: 33 AF XY: 0.0000385 AC XY: 28AN XY: 727100
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152374Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74506
ClinVar
Submissions by phenotype
Perlman syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at