Genetic Variant BCL3:c.*102_*104delCCC (chr19-44759707-GCCC-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.*102_*104delCCC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0335 in 429,770 control chromosomes in the GnomAD database, including 854 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.13 ( 2110 hom., cov: 0)

Exomes 𝑓: 0.034 ( 854 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 (AFR) allele frequency at 95% confidence interval = 0.31 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.102_104delCCC		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.102_104delCCC	3_prime_UTR	Exon 9 of 9	ENSP00000164227.5	P20749
BCL3	ENST00000474300.1	TSL:2	n.711_713delCCC	non_coding_transcript_exon	Exon 4 of 4
BCL3	ENST00000444487.1	TSL:5	c.245_247delCCC	downstream_gene	N/A	ENSP00000393731.1	H7C0A2

Frequencies

GnomAD3 genomes

AF:

0.129

AC:

14411

AN:

111408

Hom.:

2091

Cov.:

show subpopulations

Gnomad AFR

AF:

0.360

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0611

Gnomad ASJ

AF:

0.0401

Gnomad EAS

AF:

0.0750

Gnomad SAS

AF:

0.108

Gnomad FIN

AF:

0.0117

Gnomad MID

AF:

0.0684

Gnomad NFE

AF:

0.0186

Gnomad OTH

AF:

0.129

GnomAD4 exome

AF:

0.0335

AC:

14417

AN:

429770

Hom.:

854

AF XY:

0.0357

AC XY:

8024

AN XY:

225056

show subpopulations

African (AFR)

AF:

0.319

AC:

3445

AN:

10814

American (AMR)

AF:

0.0356

AC:

506

AN:

14220

Ashkenazi Jewish (ASJ)

AF:

0.0335

AC:

420

AN:

12522

East Asian (EAS)

AF:

0.0517

AC:

1301

AN:

25170

South Asian (SAS)

AF:

0.0852

AC:

3460

AN:

40600

European-Finnish (FIN)

AF:

0.0105

AC:

292

AN:

27684

Middle Eastern (MID)

AF:

0.0454

AC:

AN:

1872

European-Non Finnish (NFE)

AF:

0.0139

AC:

3776

AN:

272432

Other (OTH)

AF:

0.0463

AC:

1132

AN:

24456

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.549

Heterozygous variant carriers

597

1194

1792

2389

2986

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

184

276

368

460

<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:

0.130

AC:

14484

AN:

111510

Hom.:

2110

Cov.:

AF XY:

0.133

AC XY:

7008

AN XY:

52784

show subpopulations

African (AFR)

AF:

0.361

AC:

11888

AN:

32894

American (AMR)

AF:

0.0610

AC:

654

AN:

10718

Ashkenazi Jewish (ASJ)

AF:

0.0401

AC:

105

AN:

2620

East Asian (EAS)

AF:

0.0752

AC:

252

AN:

3352

South Asian (SAS)

AF:

0.108

AC:

376

AN:

3482

European-Finnish (FIN)

AF:

0.0117

AC:

AN:

5808

Middle Eastern (MID)

AF:

0.0625

AC:

AN:

176

European-Non Finnish (NFE)

AF:

0.0186

AC:

935

AN:

50350

Other (OTH)

AF:

0.132

AC:

195

AN:

1482

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.619

Heterozygous variant carriers

343

686

1028

1371

1714

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

136

272

408

544

680

<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:

0.0177

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-GCC

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