Variant rs2075387 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_016196.4(RBM19):c.2762G>A(p.Arg921Gln) variant causes a missense change. The variant allele was found at a frequency of 0.261 in 1,609,256 control chromosomes in the GnomAD database, including 56,295 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.24 ( 4788 hom., cov: 33)

Exomes 𝑓: 0.26 ( 51507 hom. )

Consequence

RBM19
NM_016196.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.72

Variant links:

Genes affected

RBM19 (HGNC:29098): (RNA binding motif protein 19) This gene encodes a nucleolar protein that contains six RNA-binding motifs. The encoded protein may be involved in regulating ribosome biogenesis. Multiple alternatively spliced variants, encoding the same protein, have been identified.[provided by RefSeq, Apr 2009]

RBM19 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0017284453).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RBM19	NM_016196.4 linkuse as main transcript	c.2762G>A	p.Arg921Gln	missense_variant	23/24	ENST00000261741.10	NP_057280.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
RBM19	ENST00000261741.10 linkuse as main transcript	c.2762G>A	p.Arg921Gln	missense_variant	23/24	1	NM_016196.4	ENSP00000261741	P1
RBM19	ENST00000392561.7 linkuse as main transcript	c.2762G>A	p.Arg921Gln	missense_variant	23/25	1		ENSP00000376344	P1
RBM19	ENST00000545145.6 linkuse as main transcript	c.2762G>A	p.Arg921Gln	missense_variant	23/25	2		ENSP00000442053	P1
RBM19	ENST00000552384.1 linkuse as main transcript	c.212G>A	p.Arg71Gln	missense_variant, NMD_transcript_variant	2/4	3		ENSP00000449604

Frequencies

GnomAD3 genomes

AF:

0.245

AC:

37231

AN:

152096

Hom.:

4782

Cov.:

show subpopulations

Gnomad AFR

AF:

0.180

Gnomad AMI

AF:

0.323

Gnomad AMR

AF:

0.207

Gnomad ASJ

AF:

0.288

Gnomad EAS

AF:

0.142

Gnomad SAS

AF:

0.298

Gnomad FIN

AF:

0.343

Gnomad MID

AF:

0.332

Gnomad NFE

AF:

0.277

Gnomad OTH

AF:

0.262

GnomAD3 exomes

AF:

0.245

AC:

59587

AN:

242782

Hom.:

7609

AF XY:

0.252

AC XY:

33098

AN XY:

131434

show subpopulations

Gnomad AFR exome

AF:

0.172

Gnomad AMR exome

AF:

0.176

Gnomad ASJ exome

AF:

0.294

Gnomad EAS exome

AF:

0.129

Gnomad SAS exome

AF:

0.286

Gnomad FIN exome

AF:

0.321

Gnomad NFE exome

AF:

0.266

Gnomad OTH exome

AF:

0.267

GnomAD4 exome

AF:

0.263

AC:

383432

AN:

1457042

Hom.:

51507

Cov.:

AF XY:

0.265

AC XY:

192028

AN XY:

724590

show subpopulations

Gnomad4 AFR exome

AF:

0.183

Gnomad4 AMR exome

AF:

0.182

Gnomad4 ASJ exome

AF:

0.287

Gnomad4 EAS exome

AF:

0.158

Gnomad4 SAS exome

AF:

0.293

Gnomad4 FIN exome

AF:

0.329

Gnomad4 NFE exome

AF:

0.267

Gnomad4 OTH exome

AF:

0.256

GnomAD4 genome

AF:

0.245

AC:

37256

AN:

152214

Hom.:

4788

Cov.:

AF XY:

0.248

AC XY:

18436

AN XY:

74414

show subpopulations

Gnomad4 AFR

AF:

0.181

Gnomad4 AMR

AF:

0.207

Gnomad4 ASJ

AF:

0.288

Gnomad4 EAS

AF:

0.143

Gnomad4 SAS

AF:

0.299

Gnomad4 FIN

AF:

0.343

Gnomad4 NFE

AF:

0.277

Gnomad4 OTH

AF:

0.259

Alfa

AF:

0.265

Hom.:

11610

Bravo

AF:

0.230

TwinsUK

AF:

0.264

AC:

978

ALSPAC

AF:

0.257

AC:

991

ESP6500AA

AF:

0.176

AC:

776

ESP6500EA

AF:

0.270

AC:

2321

ExAC

AF:

0.248

AC:

30086

Asia WGS

AF:

0.208

AC:

728

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.075

BayesDel_addAF

Benign

-0.42

BayesDel_noAF

Benign

-0.23

CADD

Uncertain

DANN

Pathogenic

1.0

DEOGEN2

Benign

0.18

T;T;T

Eigen

Uncertain

0.51

Eigen_PC

Uncertain

0.45

FATHMM_MKL

Uncertain

0.97

LIST_S2

Uncertain

0.96

.;.;D

MetaRNN

Benign

0.0017

T;T;T

MetaSVM

Benign

-0.94

MutationAssessor

Uncertain

2.0

M;M;M

MutationTaster

Benign

0.0000015

P;P;P

PrimateAI

Benign

0.41

PROVEAN

Benign

-2.0

N;N;N

REVEL

Benign

0.15

Sift

Uncertain

0.011

D;D;D

Sift4G

Uncertain

0.030

D;D;D

Polyphen

1.0

D;D;D

Vest4

0.26

MPC

0.20

ClinPred

0.020

GERP RS

5.1

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.41

gMVP

0.55

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over