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GeneBe

12-120546539-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_014868.5(RNF10):c.292C>G(p.Gln98Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000889 in 1,461,878 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000089 ( 0 hom. )

Consequence

RNF10
NM_014868.5 missense

Scores

1
4
14

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.29
Variant links:
Genes affected
RNF10 (HGNC:10055): (ring finger protein 10) The protein encoded by this gene contains a ring finger motif, which is known to be involved in protein-protein interactions. The specific function of this protein has not yet been determined. EST data suggests the existence of multiple alternatively spliced transcript variants, however, their full length nature is not known. [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=0.30712318).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RNF10NM_014868.5 linkuse as main transcriptc.292C>G p.Gln98Glu missense_variant 2/17 ENST00000325954.9
RNF10NM_001330474.2 linkuse as main transcriptc.292C>G p.Gln98Glu missense_variant 2/17

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RNF10ENST00000325954.9 linkuse as main transcriptc.292C>G p.Gln98Glu missense_variant 2/171 NM_014868.5 P1Q8N5U6-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000889
AC:
13
AN:
1461878
Hom.:
0
Cov.:
30
AF XY:
0.00000825
AC XY:
6
AN XY:
727240
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000117
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsNov 09, 2023The c.292C>G (p.Q98E) alteration is located in exon 2 (coding exon 2) of the RNF10 gene. This alteration results from a C to G substitution at nucleotide position 292, causing the glutamine (Q) at amino acid position 98 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.20
BayesDel_addAF
Uncertain
0.013
T
BayesDel_noAF
Benign
-0.22
Cadd
Benign
20
Dann
Benign
0.97
DEOGEN2
Benign
0.077
T;.;T
Eigen
Benign
-0.27
Eigen_PC
Benign
-0.14
FATHMM_MKL
Pathogenic
0.97
D
LIST_S2
Benign
0.84
T;T;T
M_CAP
Benign
0.024
T
MetaRNN
Benign
0.31
T;T;T
MetaSVM
Uncertain
-0.20
T
MutationAssessor
Uncertain
2.1
M;M;.
MutationTaster
Benign
1.0
D;D;D
PrimateAI
Benign
0.48
T
PROVEAN
Benign
-1.2
N;N;N
REVEL
Uncertain
0.32
Sift
Benign
0.45
T;T;T
Sift4G
Benign
0.65
T;T;D
Polyphen
0.0030
B;B;.
Vest4
0.35
MutPred
0.25
Loss of MoRF binding (P = 0.0259);Loss of MoRF binding (P = 0.0259);.;
MVP
0.69
MPC
0.21
ClinPred
0.28
T
GERP RS
3.1
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.29
gMVP
0.26

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1021762197; hg19: chr12-120984342; API