RNF10 p.Ser28Thr

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is The variant received 1 classification points (ACMG Germline Pathogenicity v2019). PM2BP4

The NM_014868.5(RNF10):c.82T>A (p.Ser28Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant is absent from the gnomAD population database at sites with sufficient sequencing coverage. In-silico predictor (REVEL) classifies this variant as likely benign. Splicing prediction tools (SpliceAI) predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain Significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

RNF10
NM_014868.5 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.61

Publications

0 publications found

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]

RNF10 links:

LOC128071547 (HGNC:0):

LOC128071547 links:

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new If you want to explore the variant's impact on the transcript NM_014868.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 1 points.

PM2

Absent from gnomAD (AR/unknown gene) — PM2; Absent from gnomAD at well-covered site (MOI: unknown) (threshold 0.001) — PM2 moderate.

BP4

Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); Splicing verdict: benign (Strong).; Germline computational verdict: benign (Supporting).

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_014868.5. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
RNF10	NM_014868.5	MANE Select	c.82T>A	p.Ser28Thr	missense	Exon 1 of 17	NP_055683.3
LOC128071547	NM_001414895.1	MANE Select	c.197T>A	p.Phe66Tyr	missense	Exon 1 of 1	NP_001401824.1	A0A6Q8PGS0
RNF10	NM_001330474.2		c.82T>A	p.Ser28Thr	missense	Exon 1 of 17	NP_001317403.1	Q8N5U6-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
RNF10	ENST00000325954.9	TSL:1 MANE Select	c.82T>A	p.Ser28Thr	missense	Exon 1 of 17	ENSP00000322242.4	Q8N5U6-1
ENSG00000288623	ENST00000675818.1	MANE Select	c.197T>A	p.Phe66Tyr	missense	Exon 1 of 1	ENSP00000502390.1	A0A6Q8PGS0
RNF10	ENST00000413266.6	TSL:5	c.82T>A	p.Ser28Thr	missense	Exon 1 of 17	ENSP00000415682.2	Q8N5U6-2

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 3 sources Large-scale international reference populations
GnomAD3 genomes					32
GnomAD4 exome					31
GnomAD4 genome					32

Showing 3 sources

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational Scores

Algorithm	Calibrated prediction	Prediction	Score
AlphaGenome AVI	Pathogenic	-	20
AlphaMissense	Benign	-	0.070
BayesDel_addAF	Benign	T	-0.012
BayesDel_noAF	Benign	-	-0.26
CADD	Uncertain	-	24
DANN	Uncertain	-	0.98
DEOGEN2	Benign	T	0.025
Eigen	Benign	-	-0.29
Eigen_PC	Benign	-	-0.16
FATHMM_MKL	Uncertain	D	0.89
FuncVEP CTI	Benign	-	0.017
GPN-Star LLR	N/A	-	-5.7
GPN-Star score	N/A	-	5.7
LIST_S2	Benign	T	0.74
M_CAP	Pathogenic	D	0.45
MetaRNN	Benign	T	0.27
MetaSVM	Benign	T	-0.53
Mutation Taster	N/A	polymorphism	90/10
MutationAssessor	Benign	N	0.0
PhyloP100	Benign	-	2.6
popEVE	Benign	-	-3.4
PrimateAI	Uncertain	T	0.71
PromoterAI	N/A	Neutral	0.020
PROVEAN	Benign	N	-0.64
REVEL	Benign	-	0.25
Sift	Benign	T	0.13
Sift4G	Benign	T	0.55
Varity_R	N/A	-	0.17
VESM-3B	Benign	-	-3.7

Showing 29 of 29 scores

Splicing Scores

Algorithm	Calibrated prediction	Prediction	Score
Pangolin (max)	Benign	-	0.0
SpliceAI score (max)	Benign	- Details are displayed if max score is > 0.2	0.0

Showing 2 of 2 scores

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACMG Germline Pathogenicity v2019

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational Scores

Splicing Scores

Publications

Other links and lift over