rs1555798029
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_005619.5(RTN2):c.834A>G(p.Leu278Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000687 in 1,456,404 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 Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
RTN2
NM_005619.5 synonymous
NM_005619.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.23
Publications
0 publications found
Genes affected
RTN2 (HGNC:10468): (reticulon 2) This gene belongs to the family of reticulon encoding genes. Reticulons are associated with the endoplasmic reticulum, and are involved in neuroendocrine secretion or in membrane trafficking in neuroendocrine cells. Reticulon proteins also play an important role in the replication of positive-strand RNA (ssRNA) viruses. Mutations at this locus have been associated with autosomal dominant spastic paraplegia-12. [provided by RefSeq, Aug 2020]
PPM1N (HGNC:26845): (protein phosphatase, Mg2+/Mn2+ dependent 1N (putative)) Predicted to enable metal ion binding activity and protein serine/threonine phosphatase activity. Predicted to be involved in negative regulation of I-kappaB kinase/NF-kappaB signaling and positive regulation of canonical Wnt signaling pathway. Predicted to be active in cytosol and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_005619.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| RTN2 | NM_005619.5 | MANE Select | c.834A>G | p.Leu278Leu | synonymous | Exon 5 of 11 | NP_005610.1 | ||
| RTN2 | NM_206900.3 | c.814+807A>G | intron | N/A | NP_996783.1 | ||||
| RTN2 | NM_206901.3 | c.-187A>G | upstream_gene | N/A | NP_996784.1 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| RTN2 | ENST00000245923.9 | TSL:1 MANE Select | c.834A>G | p.Leu278Leu | synonymous | Exon 5 of 11 | ENSP00000245923.3 | ||
| RTN2 | ENST00000344680.8 | TSL:1 | c.814+807A>G | intron | N/A | ENSP00000345127.3 | |||
| RTN2 | ENST00000591286.5 | TSL:1 | n.*31+759A>G | intron | N/A | ENSP00000467863.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1456404Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 724902 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1456404
Hom.:
Cov.:
31
AF XY:
AC XY:
1
AN XY:
724902
show subpopulations
African (AFR)
AF:
AC:
0
AN:
32918
American (AMR)
AF:
AC:
0
AN:
42334
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25970
East Asian (EAS)
AF:
AC:
0
AN:
39656
South Asian (SAS)
AF:
AC:
0
AN:
85710
European-Finnish (FIN)
AF:
AC:
0
AN:
53348
Middle Eastern (MID)
AF:
AC:
0
AN:
5754
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1110578
Other (OTH)
AF:
AC:
0
AN:
60136
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Dec 12, 2016
Athena Diagnostics
Significance:Uncertain significance
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: 19
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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