12-120534953-T-G
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014868.5(RNF10):āc.142T>Gā(p.Ser48Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0000288 in 1,599,604 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000039 ( 0 hom., cov: 32)
Exomes š: 0.000028 ( 0 hom. )
Consequence
RNF10
NM_014868.5 missense
NM_014868.5 missense
Scores
1
8
10
Clinical Significance
Conservation
PhyloP100: 5.12
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 Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.04667154).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF10 | NM_014868.5 | c.142T>G | p.Ser48Ala | missense_variant | 1/17 | ENST00000325954.9 | |
LOC128071547 | NM_001414895.1 | c.257T>G | p.Val86Gly | missense_variant | 1/1 | ENST00000675818.1 | |
RNF10 | NM_001330474.2 | c.142T>G | p.Ser48Ala | missense_variant | 1/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF10 | ENST00000325954.9 | c.142T>G | p.Ser48Ala | missense_variant | 1/17 | 1 | NM_014868.5 | P1 | |
ENST00000675818.1 | c.257T>G | p.Val86Gly | missense_variant | 1/1 | NM_001414895.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 152040Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000718 AC: 16AN: 222958Hom.: 1 AF XY: 0.0000806 AC XY: 10AN XY: 124022
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GnomAD4 exome AF: 0.0000276 AC: 40AN: 1447450Hom.: 0 Cov.: 31 AF XY: 0.0000430 AC XY: 31AN XY: 720460
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GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74374
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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 submitter | clinical testing | Ambry Genetics | Jan 10, 2022 | The c.142T>G (p.S48A) alteration is located in exon 1 (coding exon 1) of the RNF10 gene. This alteration results from a T to G substitution at nucleotide position 142, causing the serine (S) at amino acid position 48 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T
M_CAP
Pathogenic
D
MetaRNN
Benign
T;T;T
MetaSVM
Uncertain
T
MutationAssessor
Benign
L;.;L
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
REVEL
Uncertain
Sift
Benign
T;D;T
Sift4G
Benign
T;D;T
Polyphen
P;.;.
Vest4
MutPred
Loss of phosphorylation at S48 (P = 0.0019);Loss of phosphorylation at S48 (P = 0.0019);Loss of phosphorylation at S48 (P = 0.0019);
MVP
MPC
ClinPred
T
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at