rs886054503
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005619.5(RTN2):c.*148G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
RTN2
NM_005619.5 3_prime_UTR
NM_005619.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.734
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]
RTN2 Gene-Disease associations (from GenCC):
- hereditary spastic paraplegia 12Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, PanelApp Australia, Labcorp Genetics (formerly Invitae)
- neuronopathy, distal hereditary motor, autosomal recessive 11, with spasticityInheritance: AR Classification: STRONG Submitted by: Ambry Genetics, PanelApp Australia
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
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
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| RTN2 | TSL:1 MANE Select | c.*148G>A | 3_prime_UTR | Exon 11 of 11 | ENSP00000245923.3 | O75298-1 | |||
| RTN2 | TSL:1 | c.*148G>A | 3_prime_UTR | Exon 10 of 10 | ENSP00000345127.3 | O75298-2 | |||
| RTN2 | TSL:1 | c.*148G>A | 3_prime_UTR | Exon 7 of 7 | ENSP00000398178.1 | O75298-3 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 497536Hom.: 0 Cov.: 6 AF XY: 0.00 AC XY: 0AN XY: 264088
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
497536
Hom.:
Cov.:
6
AF XY:
AC XY:
0
AN XY:
264088
African (AFR)
AF:
AC:
0
AN:
14342
American (AMR)
AF:
AC:
0
AN:
24588
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
14758
East Asian (EAS)
AF:
AC:
0
AN:
33130
South Asian (SAS)
AF:
AC:
0
AN:
53208
European-Finnish (FIN)
AF:
AC:
0
AN:
31862
Middle Eastern (MID)
AF:
AC:
0
AN:
2058
European-Non Finnish (NFE)
AF:
AC:
0
AN:
295800
Other (OTH)
AF:
AC:
0
AN:
27790
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
Hereditary spastic paraplegia 12 (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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