rs1553601267
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_152383.5(DIS3L2):c.210+10_210+17dupATCTACTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,754 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
DIS3L2
NM_152383.5 intron
NM_152383.5 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.110
Publications
0 publications found
Genes affected
DIS3L2 (HGNC:28648): (DIS3 like 3'-5' exoribonuclease 2) The protein encoded by this gene is similar in sequence to 3'/5' exonucleolytic subunits of the RNA exosome. The exosome is a large multimeric ribonucleotide complex responsible for degrading various RNA substrates. Several transcript variants, some protein-coding and some not, have been found for this gene. [provided by RefSeq, Mar 2012]
DIS3L2 Gene-Disease associations (from GenCC):
- Perlman syndromeInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, Orphanet, Labcorp Genetics (formerly Invitae), G2P
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 2-232015680-A-AATCTACTG is Benign according to our data. Variant chr2-232015680-A-AATCTACTG is described in ClinVar as Likely_benign. ClinVar VariationId is 410733.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| DIS3L2 | NM_152383.5 | c.210+10_210+17dupATCTACTG | intron_variant | Intron 3 of 20 | ENST00000325385.12 | NP_689596.4 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| DIS3L2 | ENST00000325385.12 | c.210+10_210+17dupATCTACTG | intron_variant | Intron 3 of 20 | 5 | NM_152383.5 | ENSP00000315569.7 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460754Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 726736 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1460754
Hom.:
Cov.:
30
AF XY:
AC XY:
0
AN XY:
726736
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33426
American (AMR)
AF:
AC:
0
AN:
44632
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26086
East Asian (EAS)
AF:
AC:
0
AN:
39682
South Asian (SAS)
AF:
AC:
0
AN:
86200
European-Finnish (FIN)
AF:
AC:
0
AN:
53046
Middle Eastern (MID)
AF:
AC:
0
AN:
5762
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1111570
Other (OTH)
AF:
AC:
0
AN:
60350
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Perlman syndrome Benign:1
Jun 16, 2023
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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