Variant 12-120534876-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate

The NM_014868.5(RNF10):c.65A>G(p.Asn22Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 32)

Consequence

RNF10
NM_014868.5 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.09

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:):

LOC128071547 links:

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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=0.10005766).

BP6

Variant 12-120534876-A-G is Benign according to our data. Variant chr12-120534876-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2534525.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
RNF10	NM_014868.5 linkuse as main transcript	c.65A>G	p.Asn22Ser	missense_variant	1/17	ENST00000325954.9	NP_055683.3
LOC128071547	NM_001414895.1 linkuse as main transcript	c.180A>G	p.Gln60=	synonymous_variant	1/1	ENST00000675818.1	NP_001401824.1
RNF10	NM_001330474.2 linkuse as main transcript	c.65A>G	p.Asn22Ser	missense_variant	1/17		NP_001317403.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RNF10	ENST00000325954.9 linkuse as main transcript	c.65A>G	p.Asn22Ser	missense_variant	1/17	1	NM_014868.5	ENSP00000322242	P1	Q8N5U6-1
	ENST00000675818.1 linkuse as main transcript	c.180A>G	p.Gln60=	synonymous_variant	1/1		NM_001414895.1	ENSP00000502390	P1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Apr 07, 2023

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.045

BayesDel_addAF

Benign

-0.12

BayesDel_noAF

Benign

-0.41

CADD

Benign

7.6

DANN

Benign

0.52

DEOGEN2

Benign

0.018

T;T;.

Eigen

Benign

-0.88

Eigen_PC

Benign

-0.76

FATHMM_MKL

Benign

0.057

LIST_S2

Benign

0.70

T;T;T

M_CAP

Uncertain

0.22

MetaRNN

Benign

0.10

T;T;T

MetaSVM

Benign

-0.66

MutationAssessor

Benign

0.34

N;.;N

MutationTaster

Benign

0.92

D;D;D

PrimateAI

Uncertain

0.54

PROVEAN

Benign

-0.33

N;N;N

REVEL

Benign

0.26

Sift

Benign

0.50

T;T;T

Sift4G

Benign

0.74

T;T;T

Polyphen

0.0

B;.;.

Vest4

0.062

MutPred

0.27

Gain of phosphorylation at N22 (P = 6e-04);Gain of phosphorylation at N22 (P = 6e-04);Gain of phosphorylation at N22 (P = 6e-04);

MVP

0.47

MPC

0.15

ClinPred

0.20

GERP RS

1.8

Varity_R

0.041

gMVP

0.092

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

No publications associated with this variant yet.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over