chr3-149872041-A-G
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_183381.3(RNF13):āc.208A>Gā(p.Asn70Asp) variant causes a missense change. The variant allele was found at a frequency of 0.000000696 in 1,436,096 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: not found (cov: 32)
Exomes š: 7.0e-7 ( 0 hom. )
Consequence
RNF13
NM_183381.3 missense
NM_183381.3 missense
Scores
4
15
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.34
Genes affected
RNF13 (HGNC:10057): (ring finger protein 13) The protein encoded by this gene contains a RING zinc finger, a motif known to be involved in protein-protein interactions. The specific function of this gene has not yet been determined. Alternatively spliced transcript variants that encode the same protein have been reported. A pseudogene, which is also located on chromosome 3, has been defined for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.2822601).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF13 | NM_183381.3 | c.208A>G | p.Asn70Asp | missense_variant | 4/10 | ENST00000392894.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF13 | ENST00000392894.8 | c.208A>G | p.Asn70Asp | missense_variant | 4/10 | 1 | NM_183381.3 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 6.96e-7 AC: 1AN: 1436096Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 714064
GnomAD4 exome
AF:
AC:
1
AN:
1436096
Hom.:
Cov.:
28
AF XY:
AC XY:
0
AN XY:
714064
Gnomad4 AFR exome
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Gnomad4 AMR exome
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Gnomad4 ASJ exome
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Gnomad4 EAS exome
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Gnomad4 SAS exome
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Gnomad4 FIN exome
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Gnomad4 OTH exome
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GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T;.;T;.;.;T;T
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
.;T;T;D;T;T;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L;.;.;.;.;.;.
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N;N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T;T;T;T;T
Sift4G
Benign
T;T;T;T;T;T;T;T
Polyphen
B;B;.;.;.;.;.;.
Vest4
MutPred
Gain of catalytic residue at N70 (P = 0.0868);Gain of catalytic residue at N70 (P = 0.0868);Gain of catalytic residue at N70 (P = 0.0868);Gain of catalytic residue at N70 (P = 0.0868);Gain of catalytic residue at N70 (P = 0.0868);Gain of catalytic residue at N70 (P = 0.0868);Gain of catalytic residue at N70 (P = 0.0868);Gain of catalytic residue at N70 (P = 0.0868);
MVP
MPC
0.23
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