2-85595798-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_016494.4(RNF181):c.35C>T(p.Pro12Leu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P12T) has been classified as Uncertain significance.
Frequency
Genomes: not found (cov: 32)
Consequence
RNF181
NM_016494.4 missense
NM_016494.4 missense
Scores
1
8
9
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.66
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF181 | NM_016494.4 | c.35C>T | p.Pro12Leu | missense_variant | 1/5 | ENST00000306368.9 | |
RNF181 | XM_005264359.5 | c.35C>T | p.Pro12Leu | missense_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF181 | ENST00000306368.9 | c.35C>T | p.Pro12Leu | missense_variant | 1/5 | 1 | NM_016494.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 152166Hom.: 0 Cov.: 32 FAILED QC
GnomAD3 genomes
AF:
AC:
0
AN:
152166
Hom.:
Cov.:
32
FAILED QC
Gnomad AFR
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GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ExAC
AF:
AC:
2
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T;T;T
M_CAP
Uncertain
D
MetaRNN
Uncertain
D;D;D
MetaSVM
Uncertain
D
MutationTaster
Benign
D;D
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D;D
REVEL
Uncertain
Sift
Benign
T;T;T
Sift4G
Uncertain
D;D;D
Polyphen
0.015
.;B;.
Vest4
MutPred
Loss of loop (P = 0.0128);Loss of loop (P = 0.0128);Loss of loop (P = 0.0128);
MVP
MPC
0.26
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