19-44759707-GCCCCC-GCCCCCCCC
Variant names:
Variant summary
Our verdict is . The variant received 0 ACMG points: 0P and 0B.
Uncertain significance
The NM_005178.5(BCL3):c.*102_*104dupCCC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. There is a variant allele frequency bias in the population database for this variant (GnomAdExome4), which may indicate mosaicism or somatic mutations in the reference population data. 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: 0.000016 ( 0 hom. )
Consequence
BCL3
NM_005178.5 3_prime_UTR
NM_005178.5 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.398
Publications
0 publications found
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]
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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 0 ACMG points.
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.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| BCL3 | TSL:1 MANE Select | c.*102_*104dupCCC | 3_prime_UTR | Exon 9 of 9 | ENSP00000164227.5 | P20749 | |||
| BCL3 | TSL:2 | n.711_713dupCCC | non_coding_transcript_exon | Exon 4 of 4 | |||||
| BCL3 | TSL:5 | c.*244_*245insCCC | downstream_gene | N/A | ENSP00000393731.1 | H7C0A2 |
Frequencies
GnomAD3 genomes 0.00000898 AC: 1AN: 111376Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
111376
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0000163 AC: 7AN: 429784Hom.: 0 Cov.: 0 AF XY: 0.0000178 AC XY: 4AN XY: 225070 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
7
AN:
429784
Hom.:
Cov.:
0
AF XY:
AC XY:
4
AN XY:
225070
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
10814
American (AMR)
AF:
AC:
0
AN:
14220
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
12520
East Asian (EAS)
AF:
AC:
2
AN:
25172
South Asian (SAS)
AF:
AC:
0
AN:
40608
European-Finnish (FIN)
AF:
AC:
0
AN:
27684
Middle Eastern (MID)
AF:
AC:
0
AN:
1872
European-Non Finnish (NFE)
AF:
AC:
5
AN:
272438
Other (OTH)
AF:
AC:
0
AN:
24456
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000000294053), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.304
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<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 0.00000898 AC: 1AN: 111376Hom.: 0 Cov.: 0 AF XY: 0.0000190 AC XY: 1AN XY: 52652 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
1
AN:
111376
Hom.:
Cov.:
0
AF XY:
AC XY:
1
AN XY:
52652
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
32764
American (AMR)
AF:
AC:
0
AN:
10712
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2618
East Asian (EAS)
AF:
AC:
0
AN:
3360
South Asian (SAS)
AF:
AC:
0
AN:
3484
European-Finnish (FIN)
AF:
AC:
0
AN:
5806
Middle Eastern (MID)
AF:
AC:
0
AN:
190
European-Non Finnish (NFE)
AF:
AC:
1
AN:
50358
Other (OTH)
AF:
AC:
0
AN:
1456
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 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: 0.325
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.
Publications
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Other links and lift over
dbSNP: rs67149311 ;
hg19: chr19-45262964;