rs144606152

Positions:

Variant summary

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

The NM_001123385.2(BCOR):c.1791C>T(p.His597His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0436 in 1,211,156 control chromosomes in the GnomAD database, including 977 homozygotes. There are 16,949 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.032 ( 58 hom., 1026 hem., cov: 25)

Exomes 𝑓: 0.045 ( 919 hom. 15923 hem. )

Consequence

BCOR
NM_001123385.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: -0.0260

Variant links:

Genes affected

BCOR (HGNC:20893): (BCL6 corepressor) The protein encoded by this gene was identified as an interacting corepressor of BCL6, a POZ/zinc finger transcription repressor that is required for germinal center formation and may influence apoptosis. This protein selectively interacts with the POZ domain of BCL6, but not with eight other POZ proteins. Specific class I and II histone deacetylases (HDACs) have been shown to interact with this protein, which suggests a possible link between the two classes of HDACs. Several transcript variants encoding different isoforms have been found for this gene. A pseudogene of this gene is found on chromosome Y.[provided by RefSeq, Jun 2010]

BCOR links:

BCOR (HGNC:):

BCOR links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BP6

Variant X-40073555-G-A is Benign according to our data. Variant chrX-40073555-G-A is described in ClinVar as [Benign]. Clinvar id is 95767.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-40073555-G-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.026 with no splicing effect.

BA1

GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BCOR	NM_001123385.2 linkuse as main transcript	c.1791C>T	p.His597His	synonymous_variant	4/15	ENST00000378444.9	NP_001116857.1	Q6W2J9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BCOR	ENST00000378444.9 linkuse as main transcript	c.1791C>T	p.His597His	synonymous_variant	4/15	1	NM_001123385.2	ENSP00000367705.4		Q6W2J9-1

Frequencies

GnomAD3 genomes

AF:

0.0318

AC:

3598

AN:

113134

Hom.:

Cov.:

AF XY:

0.0291

AC XY:

1028

AN XY:

35270

show subpopulations

Gnomad AFR

AF:

0.00686

Gnomad AMI

AF:

0.0131

Gnomad AMR

AF:

0.0221

Gnomad ASJ

AF:

0.0621

Gnomad EAS

AF:

0.000278

Gnomad SAS

AF:

0.0122

Gnomad FIN

AF:

0.0340

Gnomad MID

AF:

0.0625

Gnomad NFE

AF:

0.0497

Gnomad OTH

AF:

0.0379

GnomAD3 exomes

AF:

0.0345

AC:

6314

AN:

183017

Hom.:

103

AF XY:

0.0349

AC XY:

2358

AN XY:

67505

show subpopulations

Gnomad AFR exome

AF:

0.00623

Gnomad AMR exome

AF:

0.0188

Gnomad ASJ exome

AF:

0.0623

Gnomad EAS exome

AF:

0.0000721

Gnomad SAS exome

AF:

0.0126

Gnomad FIN exome

AF:

0.0372

Gnomad NFE exome

AF:

0.0517

Gnomad OTH exome

AF:

0.0431

GnomAD4 exome

AF:

0.0448

AC:

49170

AN:

1097967

Hom.:

919

Cov.:

AF XY:

0.0438

AC XY:

15923

AN XY:

363357

show subpopulations

Gnomad4 AFR exome

AF:

0.00633

Gnomad4 AMR exome

AF:

0.0187

Gnomad4 ASJ exome

AF:

0.0607

Gnomad4 EAS exome

AF:

0.0000662

Gnomad4 SAS exome

AF:

0.0140

Gnomad4 FIN exome

AF:

0.0387

Gnomad4 NFE exome

AF:

0.0506

Gnomad4 OTH exome

AF:

0.0428

GnomAD4 genome

AF:

0.0318

AC:

3594

AN:

113189

Hom.:

Cov.:

AF XY:

0.0290

AC XY:

1026

AN XY:

35335

show subpopulations

Gnomad4 AFR

AF:

0.00685

Gnomad4 AMR

AF:

0.0221

Gnomad4 ASJ

AF:

0.0621

Gnomad4 EAS

AF:

0.000279

Gnomad4 SAS

AF:

0.0122

Gnomad4 FIN

AF:

0.0340

Gnomad4 NFE

AF:

0.0496

Gnomad4 OTH

AF:

0.0368

Alfa

AF:

0.0454

Hom.:

373

Bravo

AF:

0.0294

EpiCase

AF:

0.0545

EpiControl

AF:

0.0560

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Jan 31, 2013	- -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Nov 13, 2013	- -

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 01, 2018	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

History of neurodevelopmental disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Jan 09, 2013

General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance -

Oculofaciocardiodental syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 26, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

0.48

DANN

Benign

0.48

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