rs370261055
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_StrongBP6_ModerateBP7BS1
The NM_152383.5(DIS3L2):c.2031G>A(p.Ser677=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000205 in 1,612,282 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 (★). Synonymous variant affecting the same amino acid position (i.e. S677S) 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 -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DIS3L2 | NM_152383.5 | c.2031G>A | p.Ser677= | synonymous_variant | 17/21 | ENST00000325385.12 | |
DIS3L2 | NM_001257281.2 | c.1582-9485G>A | intron_variant | ||||
DIS3L2 | NR_046476.2 | n.2104G>A | non_coding_transcript_exon_variant | 17/21 | |||
DIS3L2 | NR_046477.2 | n.2083G>A | non_coding_transcript_exon_variant | 16/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DIS3L2 | ENST00000325385.12 | c.2031G>A | p.Ser677= | synonymous_variant | 17/21 | 5 | NM_152383.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000485 AC: 12AN: 247526Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134560
GnomAD4 exome AF: 0.00000890 AC: 13AN: 1459956Hom.: 0 Cov.: 32 AF XY: 0.00000964 AC XY: 7AN XY: 726348
GnomAD4 genome ? AF: 0.000131 AC: 20AN: 152326Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74476
ClinVar
Submissions by phenotype
Perlman syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 08, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at