rs144606152

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -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

Publications

5 publications found

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 Gene-Disease associations (from GenCC):

microphthalmia, syndromic 2
Inheritance: XL, Unknown Classification: DEFINITIVE, STRONG, SUPPORTIVE, LIMITED Submitted by: Ambry Genetics, ClinGen, Illumina, Orphanet, Labcorp Genetics (formerly Invitae), G2P
microphthalmia, Lenz type
Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet

BCOR links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

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 rank	MANE	Protein	UniProt
BCOR	NM_001123385.2 link	c.1791C>T	p.His597His	synonymous_variant	Exon 4 of 15	ENST00000378444.9	NP_001116857.1	Q6W2J9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCOR	ENST00000378444.9 link	c.1791C>T	p.His597His	synonymous_variant	Exon 4 of 15	1	NM_001123385.2	ENSP00000367705.4		Q6W2J9-1

Frequencies

GnomAD3 genomes

AF:

0.0318

AC:

3598

AN:

113134

Hom.:

Cov.:

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

GnomAD2 exomes

AF:

0.0345

AC:

6314

AN:

183017

AF XY:

0.0349

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 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

African (AFR)

AF:

0.00633

AC:

167

AN:

26402

American (AMR)

AF:

0.0187

AC:

660

AN:

35207

Ashkenazi Jewish (ASJ)

AF:

0.0607

AC:

1176

AN:

19386

East Asian (EAS)

AF:

0.0000662

AC:

AN:

30206

South Asian (SAS)

AF:

0.0140

AC:

760

AN:

54148

European-Finnish (FIN)

AF:

0.0387

AC:

1559

AN:

40262

Middle Eastern (MID)

AF:

0.0607

AC:

251

AN:

4135

European-Non Finnish (NFE)

AF:

0.0506

AC:

42622

AN:

842124

Other (OTH)

AF:

0.0428

AC:

1973

AN:

46097

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

2294

4587

6881

9174

11468

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0318

AC:

3594

AN:

113189

Hom.:

Cov.:

AF XY:

0.0290

AC XY:

1026

AN XY:

35335

show subpopulations

African (AFR)

AF:

0.00685

AC:

214

AN:

31263

American (AMR)

AF:

0.0221

AC:

239

AN:

10833

Ashkenazi Jewish (ASJ)

AF:

0.0621

AC:

165

AN:

2655

East Asian (EAS)

AF:

0.000279

AC:

AN:

3582

South Asian (SAS)

AF:

0.0122

AC:

AN:

2779

European-Finnish (FIN)

AF:

0.0340

AC:

214

AN:

6297

Middle Eastern (MID)

AF:

0.0639

AC:

AN:

219

European-Non Finnish (NFE)

AF:

0.0496

AC:

2647

AN:

53328

Other (OTH)

AF:

0.0368

AC:

AN:

1548

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

132

264

396

528

660

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

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

Nov 13, 2013

Eurofins Ntd Llc (ga)

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Jan 31, 2013

Genetic Services Laboratory, University of Chicago

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

May 01, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

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

Jan 09, 2013

Ambry Genetics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

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

Oculofaciocardiodental syndrome

Benign:1

Feb 02, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

0.48

(source)

DANN

Benign

0.48

PhyloP100

-0.026

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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rs144606152

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over