2-232329873-C-T
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_152383.5(DIS3L2):c.1800C>T(p.Ala600Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,459,106 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. A600A) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
DIS3L2
NM_152383.5 synonymous
NM_152383.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.864
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 2-232329873-C-T is Benign according to our data. Variant chr2-232329873-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 463077.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.1800C>T | p.Ala600Ala | synonymous_variant | Exon 15 of 21 | ENST00000325385.12 | NP_689596.4 | |
| DIS3L2 | NM_001257281.2 | c.1582-13472C>T | intron_variant | Intron 13 of 13 | NP_001244210.1 | |||
| DIS3L2 | NR_046476.2 | n.1886-13C>T | intron_variant | Intron 14 of 20 | ||||
| DIS3L2 | NR_046477.2 | n.1862-10C>T | intron_variant | Intron 13 of 18 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| DIS3L2 | ENST00000325385.12 | c.1800C>T | p.Ala600Ala | synonymous_variant | Exon 15 of 21 | 5 | NM_152383.5 | ENSP00000315569.7 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1459106Hom.: 0 Cov.: 36 AF XY: 0.00 AC XY: 0AN XY: 725876 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1459106
Hom.:
Cov.:
36
AF XY:
AC XY:
0
AN XY:
725876
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33430
American (AMR)
AF:
AC:
0
AN:
44534
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26064
East Asian (EAS)
AF:
AC:
0
AN:
39556
South Asian (SAS)
AF:
AC:
0
AN:
85854
European-Finnish (FIN)
AF:
AC:
0
AN:
52592
Middle Eastern (MID)
AF:
AC:
0
AN:
5752
European-Non Finnish (NFE)
AF:
AC:
2
AN:
1111032
Other (OTH)
AF:
AC:
0
AN:
60292
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
1
1
2
2
3
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
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>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 13, 2017
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
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: 13
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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