RNF10 p.Ser28Thr

Variant names:

• chr12-120534893-T-A
• NM_014868.5:c.82T>A
• RNF10 p.Ser28Thr

Your query was ambiguous. Multiple possible variants found:

• chr12-120534893-T-A
• chr12-120534893-TCG-ACA
• chr12-120534893-TCG-ACC
• chr12-120534893-TCG-ACT

GermlineCancer (beta)

Variant summary

Our verdict is Uncertain significance.

+1 Uncertain · Cold

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

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
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.61
• Publications: 0 publications found

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]

LOC128071547 (HGNC:0):

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript:

Our verdict: Uncertain_significance. The variant received 1 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	PM2Absent/extremely low in population databases		Absent from gnomAD (AR/unknown gene) — PM2; Absent from gnomAD at well-covered site (MOI: unknown) (threshold 0.001) — PM2 moderate.
	BP4Computational evidence suggests no impact		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

Sel.	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	Prot: NP_055683.3
	LOC128071547 NM_001414895.1	MANE Select	c.197T>A p.Phe66Tyr	missense	Exon 1 of 1	Prot: NP_001401824.1 UniProt:
	RNF10 NM_001330474.2		c.82T>A p.Ser28Thr	missense	Exon 1 of 17	Prot: NP_001317403.1 UniProt:

RNF10 NM_014868.5

MANE Select

HGVSc / HGVSpc.82T>Ap.Ser28Thr

Exon rankExon 1 of 17

missense

Prot: NP_055683.3

LOC128071547 NM_001414895.1

MANE Select

HGVSc / HGVSpc.197T>Ap.Phe66Tyr

Exon rankExon 1 of 1

missense

Prot: NP_001401824.1UniProt: A0A6Q8PGS0

RNF10 NM_001330474.2

HGVSc / HGVSpc.82T>Ap.Ser28Thr

Exon rankExon 1 of 17

missense

Prot: NP_001317403.1UniProt: Q8N5U6-2

Ensembl Transcripts

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

RNF10 ENST00000325954.9

TSL:1MANE Select

HGVSc / HGVSpc.82T>Ap.Ser28Thr

Exon rankExon 1 of 17

missense

Prot: ENSP00000322242.4UniProt: Q8N5U6-1

ENSG00000288623 ENST00000675818.1

MANE Select

HGVSc / HGVSpc.197T>Ap.Phe66Tyr

Exon rankExon 1 of 1

missense

Prot: ENSP00000502390.1UniProt: A0A6Q8PGS0

RNF10 ENST00000413266.6

TSL:5

HGVSc / HGVSpc.82T>Ap.Ser28Thr

Exon rankExon 1 of 17

missense

Prot: ENSP00000415682.2UniProt: 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	AF:	AC:	Hom:	AN:	Cov:32
GnomAD4 exome	AF:	AC:	Hom:	AN:	Cov:31
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:32

Showing 3 sources

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational Scores

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

Showing 29 of 29 scores

Splicing Scores

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

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.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Other links and lift over

hg19: chr12-120972696;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar