18-32092831-C-T
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_016271.5(RNF138):c.55C>T(p.Pro19Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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
RNF138
NM_016271.5 missense
NM_016271.5 missense
Scores
5
5
8
Clinical Significance
Conservation
PhyloP100: 2.71
Publications
0 publications found
Genes affected
RNF138 (HGNC:17765): (ring finger protein 138) The protein encoded by this gene contains a RING finger, a motif present in a variety of functionally distinct proteins and known to be involved in protein-DNA and protein-protein interactions. Alternatively spliced transcript variants encoding distinct isoforms have been observed. [provided by RefSeq, Jul 2008]
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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_016271.5. 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 |
|---|---|---|---|---|---|---|---|---|---|
| RNF138 | TSL:1 MANE Select | c.55C>T | p.Pro19Ser | missense | Exon 2 of 8 | ENSP00000261593.3 | Q8WVD3-1 | ||
| RNF138 | c.55C>T | p.Pro19Ser | missense | Exon 2 of 8 | ENSP00000637891.1 | ||||
| RNF138 | c.55C>T | p.Pro19Ser | missense | Exon 1 of 7 | ENSP00000581747.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1448592Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 720072
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1448592
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
720072
African (AFR)
AF:
AC:
0
AN:
33126
American (AMR)
AF:
AC:
0
AN:
43186
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25926
East Asian (EAS)
AF:
AC:
0
AN:
39300
South Asian (SAS)
AF:
AC:
0
AN:
83710
European-Finnish (FIN)
AF:
AC:
0
AN:
49708
Middle Eastern (MID)
AF:
AC:
0
AN:
5754
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1107876
Other (OTH)
AF:
AC:
0
AN:
60006
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
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Uncertain
D
M_CAP
Pathogenic
D
MetaRNN
Uncertain
D
MetaSVM
Benign
T
MutationAssessor
Benign
L
PhyloP100
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
D
REVEL
Uncertain
Sift
Pathogenic
D
Sift4G
Benign
T
Polyphen
P
Vest4
MutPred
Loss of helix (P = 0.1299)
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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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