Variant rs1056932 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001706.5(BCL6):c.1161C>T(p.Asn387=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 1,613,920 control chromosomes in the GnomAD database, including 341,613 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.54 ( 25905 hom., cov: 31)

Exomes 𝑓: 0.65 ( 315708 hom. )

Consequence

BCL6
NM_001706.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.773

Variant links:

Genes affected

BCL6 (HGNC:1001): (BCL6 transcription repressor) The protein encoded by this gene is a zinc finger transcription factor and contains an N-terminal POZ domain. This protein acts as a sequence-specific repressor of transcription, and has been shown to modulate the transcription of STAT-dependent IL-4 responses of B cells. This protein can interact with a variety of POZ-containing proteins that function as transcription corepressors. This gene is found to be frequently translocated and hypermutated in diffuse large-cell lymphoma (DLCL), and may be involved in the pathogenesis of DLCL. Alternatively spliced transcript variants encoding different protein isoforms have been found for this gene. [provided by RefSeq, Aug 2015]

BCL6 links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.61).

BP7

Synonymous conserved (PhyloP=0.773 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BCL6	NM_001706.5 linkuse as main transcript	c.1161C>T	p.Asn387=	synonymous_variant	5/10	ENST00000406870.7	NP_001697.2
LOC100131635	NR_034062.1 linkuse as main transcript	n.294-3127G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BCL6	ENST00000406870.7 linkuse as main transcript	c.1161C>T	p.Asn387=	synonymous_variant	5/10	1	NM_001706.5	ENSP00000384371	P1	P41182-1
	ENST00000449623.5 linkuse as main transcript	n.347-4280G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.539

AC:

81937

AN:

151936

Hom.:

25893

Cov.:

show subpopulations

Gnomad AFR

AF:

0.184

Gnomad AMI

AF:

0.802

Gnomad AMR

AF:

0.701

Gnomad ASJ

AF:

0.710

Gnomad EAS

AF:

0.798

Gnomad SAS

AF:

0.653

Gnomad FIN

AF:

0.701

Gnomad MID

AF:

0.731

Gnomad NFE

AF:

0.652

Gnomad OTH

AF:

0.596

GnomAD3 exomes

AF:

0.658

AC:

165326

AN:

251440

Hom.:

56873

AF XY:

0.661

AC XY:

89774

AN XY:

135900

show subpopulations

Gnomad AFR exome

AF:

0.169

Gnomad AMR exome

AF:

0.776

Gnomad ASJ exome

AF:

0.702

Gnomad EAS exome

AF:

0.797

Gnomad SAS exome

AF:

0.652

Gnomad FIN exome

AF:

0.694

Gnomad NFE exome

AF:

0.659

Gnomad OTH exome

AF:

0.676

GnomAD4 exome

AF:

0.651

AC:

951884

AN:

1461866

Hom.:

315708

Cov.:

AF XY:

0.652

AC XY:

474009

AN XY:

727232

show subpopulations

Gnomad4 AFR exome

AF:

0.160

Gnomad4 AMR exome

AF:

0.769

Gnomad4 ASJ exome

AF:

0.702

Gnomad4 EAS exome

AF:

0.824

Gnomad4 SAS exome

AF:

0.646

Gnomad4 FIN exome

AF:

0.690

Gnomad4 NFE exome

AF:

0.652

Gnomad4 OTH exome

AF:

0.645

GnomAD4 genome

AF:

0.539

AC:

81972

AN:

152054

Hom.:

25905

Cov.:

AF XY:

0.549

AC XY:

40771

AN XY:

74304

show subpopulations

Gnomad4 AFR

AF:

0.184

Gnomad4 AMR

AF:

0.702

Gnomad4 ASJ

AF:

0.710

Gnomad4 EAS

AF:

0.799

Gnomad4 SAS

AF:

0.655

Gnomad4 FIN

AF:

0.701

Gnomad4 NFE

AF:

0.652

Gnomad4 OTH

AF:

0.597

Alfa

AF:

0.628

Hom.:

41879

Bravo

AF:

0.525

Asia WGS

AF:

0.669

AC:

2327

AN:

3478

EpiCase

AF:

0.666

EpiControl

AF:

0.669

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

5.9

DANN

Benign

0.84

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over