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:

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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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_181844.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCL6B	NM_181844.4	MANE Select	c.*1202A>C		3_prime_UTR	Exon 9 of 9	NP_862827.2	Q8N143

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BCL6B	ENST00000293805.10	TSL:1 MANE Select	c.*1202A>C	3_prime_UTR	Exon 9 of 9	ENSP00000293805.5	Q8N143
BCL6B	ENST00000896967.1		c.*1202A>C	3_prime_UTR	Exon 9 of 9	ENSP00000567026.1
BCL6B	ENST00000896964.1		c.*1202A>C	3_prime_UTR	Exon 9 of 9	ENSP00000567024.1

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over