dbSNP rs10521149: BCL6B:c.*1202A>C (chr17-7028821-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_181844.4(BCL6B):c.*1202A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0626 in 985,372 control chromosomes in the GnomAD database, including 1,927 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 0.054 ( 234 hom., cov: 33)

Exomes 𝑓: 0.064 ( 1693 hom. )

Consequence

BCL6B
NM_181844.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.557

Publications

10 publications found

Variant links:

Genes affected

BCL6B (HGNC:1002): (BCL6B transcription repressor) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in several processes, including regulation of gene expression; regulation of inflammatory response; and type 2 immune response. Predicted to be located in nucleus. Predicted to be active in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

BCL6B links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCL6B	NM_181844.4 link	c.*1202A>C		3_prime_UTR_variant	Exon 9 of 9	ENST00000293805.10	NP_862827.2	Q8N143A8KA13

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
BCL6B	ENST00000293805.10 link	c.*1202A>C	3_prime_UTR_variant	Exon 9 of 9	1	NM_181844.4	ENSP00000293805.5	Q8N143
BCL6B	ENST00000537931.2 link	c.391-995A>C	intron_variant	Intron 3 of 3	3		ENSP00000445010.2	H0YGW0
BCL6B	ENST00000571729.1 link	n.298-995A>C	intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes

AF:

0.0543

AC:

8257

AN:

152160

Hom.:

235

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0500

Gnomad AMI

AF:

0.0252

Gnomad AMR

AF:

0.0388

Gnomad ASJ

AF:

0.0429

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.0348

Gnomad FIN

AF:

0.0530

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.0666

Gnomad OTH

AF:

0.0613

GnomAD4 exome

AF:

0.0641

AC:

53439

AN:

833094

Hom.:

1693

Cov.:

AF XY:

0.0643

AC XY:

24727

AN XY:

384710

show subpopulations

African (AFR)

AF:

0.0526

AC:

831

AN:

15786

American (AMR)

AF:

0.0427

AC:

AN:

984

Ashkenazi Jewish (ASJ)

AF:

0.0532

AC:

274

AN:

5152

East Asian (EAS)

AF:

0.000275

AC:

AN:

3630

South Asian (SAS)

AF:

0.0396

AC:

652

AN:

16460

European-Finnish (FIN)

AF:

0.0870

AC:

AN:

276

Middle Eastern (MID)

AF:

0.0679

AC:

110

AN:

1620

European-Non Finnish (NFE)

AF:

0.0656

AC:

50016

AN:

761888

Other (OTH)

AF:

0.0545

AC:

1489

AN:

27298

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

3022

6044

9065

12087

15109

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2550

5100

7650

10200

12750

<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:

0.0542

AC:

8259

AN:

152278

Hom.:

234

Cov.:

AF XY:

0.0528

AC XY:

3933

AN XY:

74462

show subpopulations

African (AFR)

AF:

0.0500

AC:

2078

AN:

41560

American (AMR)

AF:

0.0388

AC:

594

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0429

AC:

149

AN:

3470

East Asian (EAS)

AF:

0.00135

AC:

AN:

5186

South Asian (SAS)

AF:

0.0348

AC:

168

AN:

4828

European-Finnish (FIN)

AF:

0.0530

AC:

562

AN:

10612

Middle Eastern (MID)

AF:

0.0782

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0666

AC:

4527

AN:

68012

Other (OTH)

AF:

0.0607

AC:

128

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

406

811

1217

1622

2028

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

200

300

400

500

<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:

0.0628

Hom.:

596

Bravo

AF:

0.0543

Asia WGS

AF:

0.0250

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

5.3

(source)

DANN

Benign

0.41

PhyloP100

0.56

Mutation Taster

=100/0

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