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GeneBe

X-40052319-G-A

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001123385.2(BCOR):c.5058C>T(p.Asn1686=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000686 in 1,210,138 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 35 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00013 ( 0 hom., 1 hem., cov: 23)
Exomes 𝑓: 0.000062 ( 0 hom. 34 hem. )

Consequence

BCOR
NM_001123385.2 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0270
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant X-40052319-G-A is Benign according to our data. Variant chrX-40052319-G-A is described in ClinVar as [Benign]. Clinvar id is 1581317.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-40052319-G-A is described in Lovd as [Likely_benign].
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.027 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Hemizygotes in GnomAdExome at 8 XL gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BCORNM_001123385.2 linkuse as main transcriptc.5058C>T p.Asn1686= synonymous_variant 15/15 ENST00000378444.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BCORENST00000378444.9 linkuse as main transcriptc.5058C>T p.Asn1686= synonymous_variant 15/151 NM_001123385.2 P2Q6W2J9-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000133
AC:
15
AN:
112385
Hom.:
0
Cov.:
23
AF XY:
0.0000289
AC XY:
1
AN XY:
34549
show subpopulations
Gnomad AFR
AF:
0.000259
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000277
Gnomad SAS
AF:
0.000729
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000750
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000818
AC:
15
AN:
183452
Hom.:
0
AF XY:
0.000118
AC XY:
8
AN XY:
67908
show subpopulations
Gnomad AFR exome
AF:
0.000228
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000722
Gnomad SAS exome
AF:
0.000367
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000488
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000619
AC:
68
AN:
1097702
Hom.:
0
Cov.:
30
AF XY:
0.0000936
AC XY:
34
AN XY:
363062
show subpopulations
Gnomad4 AFR exome
AF:
0.000114
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000331
Gnomad4 SAS exome
AF:
0.000684
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000238
Gnomad4 OTH exome
AF:
0.000152
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000133
AC:
15
AN:
112436
Hom.:
0
Cov.:
23
AF XY:
0.0000289
AC XY:
1
AN XY:
34610
show subpopulations
Gnomad4 AFR
AF:
0.000258
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000278
Gnomad4 SAS
AF:
0.000731
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000750
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000142
Hom.:
0
Bravo
AF:
0.0000945

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Oculofaciocardiodental syndrome Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeMar 03, 2023- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.66
Cadd
Benign
0.15
Dann
Benign
0.72

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.

Other links and lift over

dbSNP: rs369322807; hg19: chrX-39911572; API