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rs113588421

chrX-40052340-T-AchrX-40052340-T-C

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_001123385.2(BCOR):c.5037A>T(p.Ile1679=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00015 in 1,210,107 control chromosomes in the GnomAD database, including 3 homozygotes. There are 60 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00049 ( 0 hom., 20 hem., cov: 23)
Exomes 𝑓: 0.00012 ( 3 hom. 40 hem. )

Consequence

BCOR
NM_001123385.2 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0180
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 -15 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=-0.5).
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-40052340-T-A is Benign according to our data. Variant chrX-40052340-T-A is described in ClinVar as [Benign]. Clinvar id is 465162.Status of the report is criteria_provided_single_submitter, 1 stars.
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=-0.018 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.000116 (127/1098023) while in subpopulation AFR AF= 0.00223 (59/26399). AF 95% confidence interval is 0.00178. There are 3 homozygotes in gnomad4_exome. There are 40 alleles in male gnomad4_exome subpopulation. Median coverage is 30. This position pass quality control queck.
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 GnomAd at 15 XL gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BCORNM_001123385.2 linkuse as main transcriptc.5037A>T p.Ile1679= synonymous_variant 15/15 ENST00000378444.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BCORENST00000378444.9 linkuse as main transcriptc.5037A>T p.Ile1679= synonymous_variant 15/151 NM_001123385.2 P2Q6W2J9-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000446
AC:
50
AN:
112031
Hom.:
0
Cov.:
23
AF XY:
0.000439
AC XY:
15
AN XY:
34189
show subpopulations
Gnomad AFR
AF:
0.00133
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000379
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000751
Gnomad OTH
AF:
0.000665
GnomAD3 exomes
AF:
0.000131
AC:
24
AN:
183469
Hom.:
0
AF XY:
0.0000883
AC XY:
6
AN XY:
67919
show subpopulations
Gnomad AFR exome
AF:
0.00137
Gnomad AMR exome
AF:
0.000182
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000122
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000116
AC:
127
AN:
1098023
Hom.:
3
Cov.:
30
AF XY:
0.000110
AC XY:
40
AN XY:
363377
show subpopulations
Gnomad4 AFR exome
AF:
0.00223
Gnomad4 AMR exome
AF:
0.000256
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000594
Gnomad4 OTH exome
AF:
0.00117
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000491
AC:
55
AN:
112084
Hom.:
0
Cov.:
23
AF XY:
0.000584
AC XY:
20
AN XY:
34252
show subpopulations
Gnomad4 AFR
AF:
0.00149
Gnomad4 AMR
AF:
0.000379
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000751
Gnomad4 OTH
AF:
0.000657
Bravo
AF:
0.000586

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 28, 2022- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.50
Cadd
Benign
4.1
Dann
Benign
0.70

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: rs113588421; hg19: chrX-39911593; API