dbSNP rs1056932: BCL6:p.Asn387Asn (chr3-187729244-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001706.5(BCL6):c.1161C>T(p.Asn387Asn) 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

Publications

40 publications found

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:

ENSG00000228804 (HGNC:):

ENSG00000228804 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
BCL6	NM_001706.5 link	c.1161C>T	p.Asn387Asn	synonymous_variant	Exon 5 of 10	ENST00000406870.7	NP_001697.2	P41182-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCL6	ENST00000406870.7 link	c.1161C>T	p.Asn387Asn	synonymous_variant	Exon 5 of 10	1	NM_001706.5	ENSP00000384371.2		P41182-1

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

GnomAD2 exomes

AF:

0.658

AC:

165326

AN:

251440

AF XY:

0.661

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 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

African (AFR)

AF:

0.160

AC:

5344

AN:

33480

American (AMR)

AF:

0.769

AC:

34409

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.702

AC:

18360

AN:

26136

East Asian (EAS)

AF:

0.824

AC:

32727

AN:

39700

South Asian (SAS)

AF:

0.646

AC:

55701

AN:

86258

European-Finnish (FIN)

AF:

0.690

AC:

36830

AN:

53404

Middle Eastern (MID)

AF:

0.694

AC:

4004

AN:

5766

European-Non Finnish (NFE)

AF:

0.652

AC:

725547

AN:

1112002

Other (OTH)

AF:

0.645

AC:

38962

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

22876

45752

68628

91504

114380

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

18908

37816

56724

75632

94540

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.539

AC:

81972

AN:

152054

Hom.:

25905

Cov.:

AF XY:

0.549

AC XY:

40771

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.184

AC:

7637

AN:

41524

American (AMR)

AF:

0.702

AC:

10734

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.710

AC:

2462

AN:

3468

East Asian (EAS)

AF:

0.799

AC:

4103

AN:

5134

South Asian (SAS)

AF:

0.655

AC:

3143

AN:

4796

European-Finnish (FIN)

AF:

0.701

AC:

7417

AN:

10574

Middle Eastern (MID)

AF:

0.724

AC:

213

AN:

294

European-Non Finnish (NFE)

AF:

0.652

AC:

44272

AN:

67942

Other (OTH)

AF:

0.597

AC:

1260

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1575

3150

4725

6300

7875

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

686

1372

2058

2744

3430

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.616

Hom.:

50120

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

(source)

DANN

Benign

0.84

PhyloP100

0.77

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=91/9

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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over