dbSNP rs67149311: BCL3:c.*100_*104delCCCCC (chr19-44759707-GCCCCC-G) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is . The variant received 2 ACMG points: 2P and 0B. PM2

The NM_005178.5(BCL3):c.*100_*104delCCCCC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000554 in 541,174 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000090 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0000047 ( 0 hom. )

Consequence

BCL3
NM_005178.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.798

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: Uncertain_significance. The variant received 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

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.100_104delCCCCC		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.100_104delCCCCC	3_prime_UTR	Exon 9 of 9	ENSP00000164227.5	P20749
BCL3	ENST00000474300.1	TSL:2	n.709_713delCCCCC	non_coding_transcript_exon	Exon 4 of 4
BCL3	ENST00000444487.1	TSL:5	c.245_249delCCCCC	downstream_gene	N/A	ENSP00000393731.1	H7C0A2

Frequencies

GnomAD3 genomes

AF:

0.00000898

AC:

AN:

111376

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000199

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00000465

AC:

AN:

429798

Hom.:

AF XY:

0.00000444

AC XY:

AN XY:

225068

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

10816

American (AMR)

AF:

0.00

AC:

AN:

14220

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

12522

East Asian (EAS)

AF:

0.00

AC:

AN:

25174

South Asian (SAS)

AF:

0.00

AC:

AN:

40610

European-Finnish (FIN)

AF:

0.00

AC:

AN:

27684

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1872

European-Non Finnish (NFE)

AF:

0.00000734

AC:

AN:

272442

Other (OTH)

AF:

0.00

AC:

AN:

24458

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.650

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.00000898

AC:

AN:

111376

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

52652

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

32764

American (AMR)

AF:

0.00

AC:

AN:

10712

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2618

East Asian (EAS)

AF:

0.00

AC:

AN:

3360

South Asian (SAS)

AF:

0.00

AC:

AN:

3484

European-Finnish (FIN)

AF:

0.00

AC:

AN:

5806

Middle Eastern (MID)

AF:

0.00

AC:

AN:

190

European-Non Finnish (NFE)

AF:

0.0000199

AC:

AN:

50358

Other (OTH)

AF:

0.00

AC:

AN:

1456

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.775

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.80

Splicing

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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over