chr2-232238530-C-T
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_152383.5(DIS3L2):c.1205-3C>T variant causes a splice region, intron change. The variant allele was found at a frequency of 0.0000174 in 1,613,350 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_152383.5 splice_region, intron
Scores
Clinical Significance
Conservation
Publications
- Perlman syndromeInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, Orphanet, Labcorp Genetics (formerly Invitae), G2P
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DIS3L2 | NM_152383.5 | c.1205-3C>T | splice_region_variant, intron_variant | Intron 10 of 20 | ENST00000325385.12 | NP_689596.4 | ||
DIS3L2 | NM_001257281.2 | c.1205-3C>T | splice_region_variant, intron_variant | Intron 10 of 13 | NP_001244210.1 | |||
DIS3L2 | NR_046476.2 | n.1351-3C>T | splice_region_variant, intron_variant | Intron 10 of 20 | ||||
DIS3L2 | NR_046477.2 | n.1327-3C>T | splice_region_variant, intron_variant | Intron 9 of 18 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152214Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000401 AC: 10AN: 249170 AF XY: 0.0000518 show subpopulations
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461136Hom.: 0 Cov.: 30 AF XY: 0.0000206 AC XY: 15AN XY: 726902 show subpopulations
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152214Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74362 show subpopulations
ClinVar
Submissions by phenotype
Perlman syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at