Variant 1-32668367-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The ENST00000373493.10(RBBP4):c.453T>C(p.Val151Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.973 in 152,258 control chromosomes in the GnomAD database, including 72,233 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.97 ( 72233 hom., cov: 31)

Exomes 𝑓: 1.0 ( 724249 hom. )

Failed GnomAD Quality Control

Consequence

RBBP4
ENST00000373493.10 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.113

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:

RBBP4 (HGNC:):

RBBP4 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.52).

BP6

Variant 1-32668367-T-C is Benign according to our data. Variant chr1-32668367-T-C is described in ClinVar as [Benign]. Clinvar id is 1263039.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.113 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RBBP4	NM_005610.3 linkuse as main transcript	c.453T>C	p.Val151Val	synonymous_variant	4/12	ENST00000373493.10	NP_005601.1	Q09028-1
RBBP4	NM_001135255.2 linkuse as main transcript	c.450T>C	p.Val150Val	synonymous_variant	4/12		NP_001128727.1	Q09028-2
RBBP4	NM_001135256.2 linkuse as main transcript	c.348T>C	p.Val116Val	synonymous_variant	4/12		NP_001128728.1	Q09028-4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RBBP4	ENST00000373493.10 linkuse as main transcript	c.453T>C	p.Val151Val	synonymous_variant	4/12	1	NM_005610.3	ENSP00000362592.4		Q09028-1

Frequencies

GnomAD3 genomes

AF:

0.973

AC:

148069

AN:

152140

Hom.:

72177

Cov.:

show subpopulations

Gnomad AFR

AF:

0.908

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.988

Gnomad ASJ

AF:

0.999

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

1.00

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

0.994

Gnomad NFE

AF:

1.00

Gnomad OTH

AF:

0.978

GnomAD3 exomes

AF:

0.993

AC:

249481

AN:

251256

Hom.:

123929

AF XY:

0.995

AC XY:

135086

AN XY:

135778

show subpopulations

Gnomad AFR exome

AF:

0.906

Gnomad AMR exome

AF:

0.995

Gnomad ASJ exome

AF:

1.00

Gnomad EAS exome

AF:

1.00

Gnomad SAS exome

AF:

1.00

Gnomad FIN exome

AF:

1.00

Gnomad NFE exome

AF:

1.00

Gnomad OTH exome

AF:

0.993

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.997

AC:

1452004

AN:

1455818

Hom.:

724249

Cov.:

AF XY:

0.998

AC XY:

723029

AN XY:

724690

show subpopulations

Gnomad4 AFR exome

AF:

0.910

Gnomad4 AMR exome

AF:

0.994

Gnomad4 ASJ exome

AF:

0.999

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

1.00

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

1.00

Gnomad4 OTH exome

AF:

0.994

GnomAD4 genome

AF:

0.973

AC:

148182

AN:

152258

Hom.:

72233

Cov.:

AF XY:

0.974

AC XY:

72509

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.908

Gnomad4 AMR

AF:

0.988

Gnomad4 ASJ

AF:

0.999

Gnomad4 EAS

AF:

1.00

Gnomad4 SAS

AF:

1.00

Gnomad4 FIN

AF:

1.00

Gnomad4 NFE

AF:

1.00

Gnomad4 OTH

AF:

0.979

Alfa

AF:

0.987

Hom.:

33512

Bravo

AF:

0.969

Asia WGS

AF:

0.997

AC:

3465

AN:

3476

EpiCase

AF:

1.00

EpiControl

AF:

1.00

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Apr 25, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.52

CADD

Benign

6.0

DANN

Benign

0.68

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