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GeneBe

12-120534864-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_014868.5(RNF10):c.53A>G(p.Asn18Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000687 in 1,456,238 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: 6.9e-7 ( 0 hom. )

Consequence

RNF10
NM_014868.5 missense

Scores

1
2
16

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.35
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 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.12240407).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RNF10NM_014868.5 linkuse as main transcriptc.53A>G p.Asn18Ser missense_variant 1/17 ENST00000325954.9
LOC128071547NM_001414895.1 linkuse as main transcriptc.168A>G p.Glu56= synonymous_variant 1/1 ENST00000675818.1
RNF10NM_001330474.2 linkuse as main transcriptc.53A>G p.Asn18Ser missense_variant 1/17

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RNF10ENST00000325954.9 linkuse as main transcriptc.53A>G p.Asn18Ser missense_variant 1/171 NM_014868.5 P1Q8N5U6-1
ENST00000675818.1 linkuse as main transcriptc.168A>G p.Glu56= synonymous_variant 1/1 NM_001414895.1 P1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000844
AC:
2
AN:
237102
Hom.:
0
AF XY:
0.00000768
AC XY:
1
AN XY:
130190
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000293
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000944
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
6.87e-7
AC:
1
AN:
1456238
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
724676
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000224
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:
0.00
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 GeneticsDec 22, 2023The c.53A>G (p.N18S) alteration is located in exon 1 (coding exon 1) of the RNF10 gene. This alteration results from a A to G substitution at nucleotide position 53, causing the asparagine (N) at amino acid position 18 to be replaced by a serine (S). 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
0.084
BayesDel_addAF
Benign
-0.11
T
BayesDel_noAF
Benign
-0.39
Cadd
Benign
18
Dann
Uncertain
0.97
DEOGEN2
Benign
0.020
T;T;.
Eigen
Benign
-0.80
Eigen_PC
Benign
-0.68
FATHMM_MKL
Benign
0.46
N
LIST_S2
Benign
0.76
T;T;T
M_CAP
Pathogenic
0.47
D
MetaRNN
Benign
0.12
T;T;T
MetaSVM
Benign
-0.57
T
MutationAssessor
Benign
-0.14
N;.;N
MutationTaster
Benign
0.93
D;D;D
PrimateAI
Uncertain
0.77
T
PROVEAN
Benign
-0.73
N;N;N
REVEL
Benign
0.21
Sift
Benign
0.14
T;D;T
Sift4G
Benign
0.68
T;T;T
Polyphen
0.0030
B;.;.
Vest4
0.15
MutPred
0.18
Gain of phosphorylation at N18 (P = 0.0013);Gain of phosphorylation at N18 (P = 0.0013);Gain of phosphorylation at N18 (P = 0.0013);
MVP
0.50
MPC
0.15
ClinPred
0.091
T
GERP RS
1.1
Varity_R
0.062
gMVP
0.24

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: rs1327493457; hg19: chr12-120972667; API