Genetic Variant BCL3:c.*101_*104delCCCC (chr19-44759707-GCCCC-G) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is . The variant received -8 ACMG points: 0P and 8B. BA1

The NM_005178.5(BCL3):c.*101_*104delCCCC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0511 in 429,750 control chromosomes in the GnomAD database, including 846 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.084 ( 443 hom., cov: 0)

Exomes 𝑓: 0.051 ( 846 hom. )

Failed GnomAD Quality Control

Consequence

BCL3
NM_005178.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.715

Publications

0 publications found

Variant links:

Genes affected

BCL3 (HGNC:998): (BCL3 transcription coactivator) This gene is a proto-oncogene candidate. It is identified by its translocation into the immunoglobulin alpha-locus in some cases of B-cell leukemia. The protein encoded by this gene contains seven ankyrin repeats, which are most closely related to those found in I kappa B proteins. This protein functions as a transcriptional co-activator that activates through its association with NF-kappa B homodimers. The expression of this gene can be induced by NF-kappa B, which forms a part of the autoregulatory loop that controls the nuclear residence of p50 NF-kappa B. [provided by RefSeq, Jul 2008]

BCL3 links:

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new If you want to explore the variant's impact on the transcript NM_005178.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAdExome4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005178.5. 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
	BCL3	NM_005178.5	MANE Select	c.101_104delCCCC		3_prime_UTR	Exon 9 of 9	NP_005169.2	P20749

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BCL3	ENST00000164227.10	TSL:1 MANE Select	c.101_104delCCCC	3_prime_UTR	Exon 9 of 9	ENSP00000164227.5	P20749
BCL3	ENST00000474300.1	TSL:2	n.710_713delCCCC	non_coding_transcript_exon	Exon 4 of 4
BCL3	ENST00000444487.1	TSL:5	c.245_248delCCCC	downstream_gene	N/A	ENSP00000393731.1	H7C0A2

Frequencies

GnomAD3 genomes

AF:

0.0840

AC:

9355

AN:

111396

Hom.:

442

Cov.:

show subpopulations

Gnomad AFR

AF:

0.123

Gnomad AMI

AF:

0.0239

Gnomad AMR

AF:

0.128

Gnomad ASJ

AF:

0.0398

Gnomad EAS

AF:

0.0265

Gnomad SAS

AF:

0.142

Gnomad FIN

AF:

0.0563

Gnomad MID

AF:

0.0526

Gnomad NFE

AF:

0.0556

Gnomad OTH

AF:

0.0865

GnomAD4 exome

AF:

0.0511

AC:

21971

AN:

429750

Hom.:

846

AF XY:

0.0546

AC XY:

12291

AN XY:

225050

show subpopulations

African (AFR)

AF:

0.104

AC:

1126

AN:

10810

American (AMR)

AF:

0.106

AC:

1504

AN:

14218

Ashkenazi Jewish (ASJ)

AF:

0.0274

AC:

343

AN:

12522

East Asian (EAS)

AF:

0.0118

AC:

298

AN:

25172

South Asian (SAS)

AF:

0.116

AC:

4721

AN:

40594

European-Finnish (FIN)

AF:

0.0368

AC:

1019

AN:

27682

Middle Eastern (MID)

AF:

0.0513

AC:

AN:

1872

European-Non Finnish (NFE)

AF:

0.0426

AC:

11608

AN:

272422

Other (OTH)

AF:

0.0514

AC:

1256

AN:

24458

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.562

Heterozygous variant carriers

919

1837

2756

3674

4593

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

240

360

480

600

<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

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0840

AC:

9362

AN:

111496

Hom.:

443

Cov.:

AF XY:

0.0873

AC XY:

4608

AN XY:

52774

show subpopulations

African (AFR)

AF:

0.122

AC:

4022

AN:

32874

American (AMR)

AF:

0.128

AC:

1370

AN:

10722

Ashkenazi Jewish (ASJ)

AF:

0.0398

AC:

104

AN:

2616

East Asian (EAS)

AF:

0.0268

AC:

AN:

3352

South Asian (SAS)

AF:

0.144

AC:

500

AN:

3482

European-Finnish (FIN)

AF:

0.0563

AC:

327

AN:

5806

Middle Eastern (MID)

AF:

0.0511

AC:

AN:

176

European-Non Finnish (NFE)

AF:

0.0556

AC:

2799

AN:

50362

Other (OTH)

AF:

0.0853

AC:

126

AN:

1478

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.633

Heterozygous variant carriers

299

598

897

1196

1495

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

108

216

324

432

540

<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:

0.0363

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.71

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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19-44759707-GCCCCC-GC

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