Variant chr5-179966867-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_018434.6(RNF130):c.1089A>G(p.Ser363=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00409 in 1,613,940 control chromosomes in the GnomAD database, including 215 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.020 ( 104 hom., cov: 33)

Exomes 𝑓: 0.0024 ( 111 hom. )

Consequence

RNF130
NM_018434.6 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.17

Variant links:

Genes affected

RNF130 (HGNC:18280): (ring finger protein 130) The protein encoded by this gene contains a RING finger motif and is similar to g1, a Drosophila zinc-finger protein that is expressed in mesoderm and involved in embryonic development. The expression of the mouse counterpart was found to be upregulated in myeloblastic cells following IL3 deprivation, suggesting that this gene may regulate growth factor withdrawal-induced apoptosis of myeloid precursor cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

RNF130 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 5-179966867-T-C is Benign according to our data. Variant chr5-179966867-T-C is described in ClinVar as [Benign]. Clinvar id is 776104.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.17 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.067 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
RNF130	NM_018434.6 linkuse as main transcript	c.1089A>G	p.Ser363=	synonymous_variant	7/9	ENST00000521389.6	NP_060904.2
RNF130	NM_001410829.1 linkuse as main transcript	c.1089A>G	p.Ser363=	synonymous_variant	7/8		NP_001397758.1
RNF130	NM_001280801.2 linkuse as main transcript	c.1089A>G	p.Ser363=	synonymous_variant	7/8		NP_001267730.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RNF130	ENST00000521389.6 linkuse as main transcript	c.1089A>G	p.Ser363=	synonymous_variant	7/9	1	NM_018434.6	ENSP00000430237	P4	Q86XS8-1
RNF130	ENST00000261947.4 linkuse as main transcript	c.1089A>G	p.Ser363=	synonymous_variant	7/8	1		ENSP00000261947	A2	Q86XS8-2
RNF130	ENST00000520911.5 linkuse as main transcript	c.*608A>G		3_prime_UTR_variant, NMD_transcript_variant	7/9	1		ENSP00000430999
RNF130	ENST00000522208.6 linkuse as main transcript	c.1089A>G	p.Ser363=	synonymous_variant	7/8	5		ENSP00000429509	A1

Frequencies

GnomAD3 genomes

AF:

0.0200

AC:

3043

AN:

152036

Hom.:

102

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0689

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00570

Gnomad ASJ

AF:

0.00548

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.000623

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.000412

Gnomad OTH

AF:

0.0201

GnomAD3 exomes

AF:

0.00542

AC:

1362

AN:

251458

Hom.:

AF XY:

0.00408

AC XY:

554

AN XY:

135908

show subpopulations

Gnomad AFR exome

AF:

0.0705

Gnomad AMR exome

AF:

0.00301

Gnomad ASJ exome

AF:

0.00308

Gnomad EAS exome

AF:

0.000381

Gnomad SAS exome

AF:

0.000653

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000316

Gnomad OTH exome

AF:

0.00310

GnomAD4 exome

AF:

0.00242

AC:

3542

AN:

1461786

Hom.:

111

Cov.:

AF XY:

0.00211

AC XY:

1538

AN XY:

727200

show subpopulations

Gnomad4 AFR exome

AF:

0.0760

Gnomad4 AMR exome

AF:

0.00380

Gnomad4 ASJ exome

AF:

0.00375

Gnomad4 EAS exome

AF:

0.000151

Gnomad4 SAS exome

AF:

0.000661

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000278

Gnomad4 OTH exome

AF:

0.00520

GnomAD4 genome

AF:

0.0201

AC:

3058

AN:

152154

Hom.:

104

Cov.:

AF XY:

0.0190

AC XY:

1414

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.0691

Gnomad4 AMR

AF:

0.00569

Gnomad4 ASJ

AF:

0.00548

Gnomad4 EAS

AF:

0.00135

Gnomad4 SAS

AF:

0.000624

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000397

Gnomad4 OTH

AF:

0.0199

Alfa

AF:

0.0127

Hom.:

Bravo

AF:

0.0228

Asia WGS

AF:

0.00837

AC:

AN:

3478

EpiCase

AF:

0.000600

EpiControl

AF:

0.000652

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 25, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.18

DANN

Benign

0.60

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over