Variant rs359955 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000373493.10(RBBP4):c.761+41A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.752 in 1,611,592 control chromosomes in the GnomAD database, including 466,787 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.

Frequency

Genomes: 𝑓 0.63 ( 34004 hom., cov: 30)

Exomes 𝑓: 0.76 ( 432783 hom. )

Consequence

RBBP4
ENST00000373493.10 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.81

Variant links:

Genes affected

RBBP4 (HGNC:9887): (RB binding protein 4, chromatin remodeling factor) This gene encodes a ubiquitously expressed nuclear protein which belongs to a highly conserved subfamily of WD-repeat proteins. It is present in protein complexes involved in histone acetylation and chromatin assembly. It is part of the Mi-2 complex which has been implicated in chromatin remodeling and transcriptional repression associated with histone deacetylation. This encoded protein is also part of co-repressor complexes, which is an integral component of transcriptional silencing. It is found among several cellular proteins that bind directly to retinoblastoma protein to regulate cell proliferation. This protein also seems to be involved in transcriptional repression of E2F-responsive genes. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2008]

RBBP4 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 (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
RBBP4	NM_005610.3 linkuse as main transcript	c.761+41A>C	intron_variant	ENST00000373493.10	NP_005601.1
RBBP4	NM_001135255.2 linkuse as main transcript	c.758+41A>C	intron_variant		NP_001128727.1
RBBP4	NM_001135256.2 linkuse as main transcript	c.656+41A>C	intron_variant		NP_001128728.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RBBP4	ENST00000373493.10 linkuse as main transcript	c.761+41A>C		intron_variant		1	NM_005610.3	ENSP00000362592	P3	Q09028-1

Frequencies

GnomAD3 genomes

AF:

0.630

AC:

95661

AN:

151784

Hom.:

34003

Cov.:

show subpopulations

Gnomad AFR

AF:

0.275

Gnomad AMI

AF:

0.888

Gnomad AMR

AF:

0.651

Gnomad ASJ

AF:

0.683

Gnomad EAS

AF:

0.745

Gnomad SAS

AF:

0.749

Gnomad FIN

AF:

0.844

Gnomad MID

AF:

0.472

Gnomad NFE

AF:

0.786

Gnomad OTH

AF:

0.620

GnomAD3 exomes

AF:

0.733

AC:

182935

AN:

249642

Hom.:

69275

AF XY:

0.741

AC XY:

99944

AN XY:

134932

show subpopulations

Gnomad AFR exome

AF:

0.264

Gnomad AMR exome

AF:

0.718

Gnomad ASJ exome

AF:

0.689

Gnomad EAS exome

AF:

0.731

Gnomad SAS exome

AF:

0.736

Gnomad FIN exome

AF:

0.848

Gnomad NFE exome

AF:

0.786

Gnomad OTH exome

AF:

0.732

GnomAD4 exome

AF:

0.765

AC:

1115976

AN:

1459690

Hom.:

432783

Cov.:

AF XY:

0.765

AC XY:

555284

AN XY:

726036

show subpopulations

Gnomad4 AFR exome

AF:

0.253

Gnomad4 AMR exome

AF:

0.709

Gnomad4 ASJ exome

AF:

0.684

Gnomad4 EAS exome

AF:

0.763

Gnomad4 SAS exome

AF:

0.732

Gnomad4 FIN exome

AF:

0.848

Gnomad4 NFE exome

AF:

0.786

Gnomad4 OTH exome

AF:

0.721

GnomAD4 genome

AF:

0.630

AC:

95688

AN:

151902

Hom.:

34004

Cov.:

AF XY:

0.633

AC XY:

47027

AN XY:

74258

show subpopulations

Gnomad4 AFR

AF:

0.275

Gnomad4 AMR

AF:

0.651

Gnomad4 ASJ

AF:

0.683

Gnomad4 EAS

AF:

0.744

Gnomad4 SAS

AF:

0.749

Gnomad4 FIN

AF:

0.844

Gnomad4 NFE

AF:

0.786

Gnomad4 OTH

AF:

0.622

Alfa

AF:

0.746

Hom.:

66557

Bravo

AF:

0.597

Asia WGS

AF:

0.710

AC:

2469

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

5.0

DANN

Benign

0.52

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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