Genetic Variant BCL3:c.*104delC (chr19-44759707-GC-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.*104delC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.072 ( 164 hom., cov: 0)

Exomes 𝑓: 0.24 ( 217 hom. )

Consequence

BCL3
NM_005178.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.398

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

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0796 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.*104delC		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.*104delC	3_prime_UTR	Exon 9 of 9	ENSP00000164227.5	P20749
BCL3	ENST00000474300.1	TSL:2	n.713delC	non_coding_transcript_exon	Exon 4 of 4
BCL3	ENST00000444487.1	TSL:5	c.*245delC	downstream_gene	N/A	ENSP00000393731.1	H7C0A2

Frequencies

GnomAD3 genomes

AF:

0.0718

AC:

7946

AN:

110672

Hom.:

165

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0824

Gnomad AMI

AF:

0.0399

Gnomad AMR

AF:

0.0552

Gnomad ASJ

AF:

0.0884

Gnomad EAS

AF:

0.0650

Gnomad SAS

AF:

0.0508

Gnomad FIN

AF:

0.0392

Gnomad MID

AF:

0.0684

Gnomad NFE

AF:

0.0737

Gnomad OTH

AF:

0.0671

GnomAD4 exome

AF:

0.241

AC:

96341

AN:

400178

Hom.:

217

Cov.:

AF XY:

0.242

AC XY:

50696

AN XY:

209550

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.137

AC:

1449

AN:

10600

American (AMR)

AF:

0.227

AC:

3041

AN:

13388

Ashkenazi Jewish (ASJ)

AF:

0.228

AC:

2669

AN:

11720

East Asian (EAS)

AF:

0.260

AC:

5986

AN:

23040

South Asian (SAS)

AF:

0.246

AC:

9479

AN:

38462

European-Finnish (FIN)

AF:

0.269

AC:

6675

AN:

24830

Middle Eastern (MID)

AF:

0.239

AC:

415

AN:

1738

European-Non Finnish (NFE)

AF:

0.242

AC:

61346

AN:

253618

Other (OTH)

AF:

0.232

AC:

5281

AN:

22782

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.359

Heterozygous variant carriers

5213

10426

15640

20853

26066

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

486

972

1458

1944

2430

<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:

0.0717

AC:

7941

AN:

110768

Hom.:

164

Cov.:

AF XY:

0.0695

AC XY:

3642

AN XY:

52426

show subpopulations

African (AFR)

AF:

0.0822

AC:

2676

AN:

32572

American (AMR)

AF:

0.0552

AC:

589

AN:

10672

Ashkenazi Jewish (ASJ)

AF:

0.0884

AC:

231

AN:

2614

East Asian (EAS)

AF:

0.0658

AC:

220

AN:

3344

South Asian (SAS)

AF:

0.0506

AC:

175

AN:

3460

European-Finnish (FIN)

AF:

0.0392

AC:

223

AN:

5694

Middle Eastern (MID)

AF:

0.0625

AC:

AN:

176

European-Non Finnish (NFE)

AF:

0.0736

AC:

3693

AN:

50144

Other (OTH)

AF:

0.0668

AC:

AN:

1466

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.449

Heterozygous variant carriers

267

534

800

1067

1334

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

172

258

344

430

<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:

0.0236

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.40

Mutation Taster

=100/0

polymorphism

(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-GCCCC

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