Variant chr4-40426074-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001098634.2(RBM47):c.1612G>A(p.Gly538Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00473 in 1,614,154 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.0035 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0049 ( 24 hom. )

Consequence

RBM47
NM_001098634.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 5.76

Variant links:

Genes affected

RBM47 (HGNC:30358): (RNA binding motif protein 47) Enables RNA binding activity. Predicted to act upstream of or within cytidine to uridine editing and hematopoietic progenitor cell differentiation. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

RBM47 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.008725107).

BP6

Variant 4-40426074-C-T is Benign according to our data. Variant chr4-40426074-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3257599.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 537 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RBM47	NM_001098634.2 linkuse as main transcript	c.1612G>A	p.Gly538Arg	missense_variant	7/7	ENST00000295971.12	NP_001092104.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RBM47	ENST00000295971.12 linkuse as main transcript	c.1612G>A	p.Gly538Arg	missense_variant	7/7	5	NM_001098634.2	ENSP00000295971	P1	A0AV96-1
	ENST00000514187.1 linkuse as main transcript			upstream_gene_variant		3

Frequencies

GnomAD3 genomes

AF:

0.00353

AC:

537

AN:

152154

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00109

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00347

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00320

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00584

Gnomad OTH

AF:

0.00382

GnomAD3 exomes

AF:

0.00368

AC:

920

AN:

249714

Hom.:

AF XY:

0.00364

AC XY:

492

AN XY:

135148

show subpopulations

Gnomad AFR exome

AF:

0.000800

Gnomad AMR exome

AF:

0.00116

Gnomad ASJ exome

AF:

0.00139

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00448

Gnomad NFE exome

AF:

0.00654

Gnomad OTH exome

AF:

0.00392

GnomAD4 exome

AF:

0.00486

AC:

7099

AN:

1461884

Hom.:

Cov.:

AF XY:

0.00471

AC XY:

3422

AN XY:

727242

show subpopulations

Gnomad4 AFR exome

AF:

0.000568

Gnomad4 AMR exome

AF:

0.00103

Gnomad4 ASJ exome

AF:

0.00161

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00477

Gnomad4 NFE exome

AF:

0.00590

Gnomad4 OTH exome

AF:

0.00285

GnomAD4 genome

AF:

0.00353

AC:

537

AN:

152270

Hom.:

Cov.:

AF XY:

0.00338

AC XY:

252

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.00108

Gnomad4 AMR

AF:

0.00347

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00320

Gnomad4 NFE

AF:

0.00584

Gnomad4 OTH

AF:

0.00378

Alfa

AF:

0.00508

Hom.:

Bravo

AF:

0.00313

TwinsUK

AF:

0.00674

AC:

ALSPAC

AF:

0.00519

AC:

ESP6500AA

AF:

0.000908

AC:

ESP6500EA

AF:

0.00605

AC:

ExAC

AF:

0.00387

AC:

470

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.00491

EpiControl

AF:

0.00492

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jul 01, 2024

RBM47: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.82

BayesDel_addAF

Benign

-0.28

BayesDel_noAF

Benign

-0.16

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.072

T;.;T;.

Eigen

Uncertain

0.60

Eigen_PC

Uncertain

0.65

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Uncertain

0.90

.;D;D;D

M_CAP

Benign

0.043

MetaRNN

Benign

0.0087

T;T;T;T

MetaSVM

Benign

-0.96

MutationAssessor

Benign

0.81

L;.;L;.

MutationTaster

Benign

1.0

D;D;D;D;D

PrimateAI

Uncertain

0.71

PROVEAN

Benign

-1.0

N;N;N;N

REVEL

Uncertain

0.31

Sift

Uncertain

0.0050

D;D;D;D

Sift4G

Benign

0.10

T;D;T;T

Polyphen

1.0

D;D;D;.

Vest4

0.64

MutPred

0.46

Gain of solvent accessibility (P = 0.0328);.;Gain of solvent accessibility (P = 0.0328);.;

MVP

0.093

MPC

1.0

ClinPred

0.034

GERP RS

6.0

Varity_R

0.054

gMVP

0.93

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