rs371733417
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_152383.5(DIS3L2):c.2154G>A(p.Ala718=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000174 in 1,608,976 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. A718A) 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 -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DIS3L2 | NM_152383.5 | c.2154G>A | p.Ala718= | synonymous_variant | 17/21 | ENST00000325385.12 | |
DIS3L2 | NM_001257281.2 | c.1582-9362G>A | intron_variant | ||||
DIS3L2 | NR_046476.2 | n.2227G>A | non_coding_transcript_exon_variant | 17/21 | |||
DIS3L2 | NR_046477.2 | n.2206G>A | non_coding_transcript_exon_variant | 16/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DIS3L2 | ENST00000325385.12 | c.2154G>A | p.Ala718= | synonymous_variant | 17/21 | 5 | NM_152383.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152180Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000698 AC: 17AN: 243682Hom.: 0 AF XY: 0.0000678 AC XY: 9AN XY: 132808
GnomAD4 exome AF: 0.0000172 AC: 25AN: 1456796Hom.: 0 Cov.: 32 AF XY: 0.0000221 AC XY: 16AN XY: 724712
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152180Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74346
ClinVar
Submissions by phenotype
Perlman syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 20, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2023 | DIS3L2: BP4, BP7 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at