20-57358991-C-T
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4
The NM_003610.4(RAE1):c.288+2453C>T variant causes a intron change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
RAE1
NM_003610.4 intron
NM_003610.4 intron
Scores
1
12
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.88
Publications
0 publications found
Genes affected
RAE1 (HGNC:9828): (ribonucleic acid export 1) Mutations in the Schizosaccharomyces pombe Rae1 and Saccharomyces cerevisiae Gle2 genes have been shown to result in accumulation of poly(A)-containing mRNA in the nucleus, suggesting that the encoded proteins are involved in RNA export. The protein encoded by this gene is a homolog of yeast Rae1. It contains four WD40 motifs, and has been shown to localize to distinct foci in the nucleoplasm, to the nuclear rim, and to meshwork-like structures throughout the cytoplasm. This gene is thought to be involved in nucleocytoplasmic transport, and in directly or indirectly attaching cytoplasmic mRNPs to the cytoskeleton. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]
MTRNR2L3 (HGNC:37157): (MT-RNR2 like 3 (pseudogene)) Predicted to enable receptor antagonist activity. Predicted to be involved in negative regulation of execution phase of apoptosis. Predicted to be located in cytoplasm and extracellular region. [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 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.37118137).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_003610.4. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD2 exomes AF: 0.00 AC: 0AN: 119058 AF XY: 0.00
GnomAD2 exomes
AF:
AC:
0
AN:
119058
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1357042Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 669484
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1357042
Hom.:
Cov.:
29
AF XY:
AC XY:
0
AN XY:
669484
African (AFR)
AF:
AC:
0
AN:
30180
American (AMR)
AF:
AC:
0
AN:
31500
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24264
East Asian (EAS)
AF:
AC:
0
AN:
34160
South Asian (SAS)
AF:
AC:
0
AN:
74206
European-Finnish (FIN)
AF:
AC:
0
AN:
36848
Middle Eastern (MID)
AF:
AC:
0
AN:
3966
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1065582
Other (OTH)
AF:
AC:
0
AN:
56336
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
PhyloP100
PROVEAN
Pathogenic
D
REVEL
Benign
Vest4
MVP
ClinPred
D
GERP RS
Varity_R
gMVP
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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