Genetic Variant BCOR:c.*299_*300dupAA (chrX-40051808-A-ATT) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001123385.2(BCOR):c.*299_*300dupAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.19 ( 1610 hom., 5127 hem., cov: 18)

Exomes 𝑓: 0.13 ( 584 hom. 2257 hem. )

Consequence

BCOR
NM_001123385.2 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.603

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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant X-40051808-A-ATT is Benign according to our data. Variant chrX-40051808-A-ATT is described in ClinVar as [Benign]. Clinvar id is 1228197.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCOR	NM_001123385.2 link	c.299_300dupAA		3_prime_UTR_variant	Exon 15 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.299_300dupAA		3_prime_UTR_variant	Exon 15 of 15	1	NM_001123385.2	ENSP00000367705.4		Q6W2J9-1

Frequencies

GnomAD3 genomes

AF:

0.187

AC:

20429

AN:

109144

Hom.:

1612

Cov.:

show subpopulations

Gnomad AFR

AF:

0.216

Gnomad AMI

AF:

0.418

Gnomad AMR

AF:

0.140

Gnomad ASJ

AF:

0.180

Gnomad EAS

AF:

0.000562

Gnomad SAS

AF:

0.170

Gnomad FIN

AF:

0.0887

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.202

Gnomad OTH

AF:

0.171

GnomAD4 exome

AF:

0.133

AC:

15148

AN:

113882

Hom.:

584

Cov.:

AF XY:

0.0825

AC XY:

2257

AN XY:

27344

show subpopulations

African (AFR)

AF:

0.173

AC:

722

AN:

4185

American (AMR)

AF:

0.0903

AC:

448

AN:

4960

Ashkenazi Jewish (ASJ)

AF:

0.134

AC:

631

AN:

4708

East Asian (EAS)

AF:

0.0000838

AC:

AN:

11929

South Asian (SAS)

AF:

0.106

AC:

245

AN:

2320

European-Finnish (FIN)

AF:

0.0868

AC:

448

AN:

5163

Middle Eastern (MID)

AF:

0.182

AC:

AN:

501

European-Non Finnish (NFE)

AF:

0.158

AC:

11320

AN:

71806

Other (OTH)

AF:

0.149

AC:

1242

AN:

8310

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.443

Heterozygous variant carriers

505

1010

1516

2021

2526

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.187

AC:

20417

AN:

109186

Hom.:

1610

Cov.:

AF XY:

0.161

AC XY:

5127

AN XY:

31804

show subpopulations

African (AFR)

AF:

0.216

AC:

6470

AN:

29960

American (AMR)

AF:

0.140

AC:

1428

AN:

10188

Ashkenazi Jewish (ASJ)

AF:

0.180

AC:

469

AN:

2605

East Asian (EAS)

AF:

0.000564

AC:

AN:

3548

South Asian (SAS)

AF:

0.169

AC:

434

AN:

2573

European-Finnish (FIN)

AF:

0.0887

AC:

502

AN:

5658

Middle Eastern (MID)

AF:

0.191

AC:

AN:

209

European-Non Finnish (NFE)

AF:

0.202

AC:

10549

AN:

52310

Other (OTH)

AF:

0.168

AC:

249

AN:

1480

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

583

1165

1748

2330

2913

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0812

Hom.:

384

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Aug 31, 2019

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.60

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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chrX-40051808-A-ATT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over