19-44759707-GCCCCC-GCCCCCC
Variant names:
Variant summary
Our verdict is . The variant received -8 ACMG points: 0P and 8B. BA1
Benign
The NM_005178.5(BCL3):c.*104dupC 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 0.14 ( 1560 hom., cov: 0)
Exomes 𝑓: 0.16 ( 31 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]
Genome browser will be placed here
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 (NFE) allele frequency at 95% confidence interval = 0.17 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.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| BCL3 | TSL:1 MANE Select | c.*104dupC | 3_prime_UTR | Exon 9 of 9 | ENSP00000164227.5 | P20749 | |||
| BCL3 | TSL:2 | n.713dupC | non_coding_transcript_exon | Exon 4 of 4 | |||||
| BCL3 | TSL:5 | c.*244_*245insC | downstream_gene | N/A | ENSP00000393731.1 | H7C0A2 |
Frequencies
GnomAD3 genomes 0.136 AC: 14922AN: 110086Hom.: 1559 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
14922
AN:
110086
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: 0.155 AC: 65286AN: 420360Hom.: 31 Cov.: 0 AF XY: 0.151 AC XY: 33343AN XY: 220130 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
65286
AN:
420360
Hom.:
Cov.:
0
AF XY:
AC XY:
33343
AN XY:
220130
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
1086
AN:
10564
American (AMR)
AF:
AC:
1803
AN:
13966
Ashkenazi Jewish (ASJ)
AF:
AC:
2642
AN:
12168
East Asian (EAS)
AF:
AC:
4317
AN:
24444
South Asian (SAS)
AF:
AC:
3292
AN:
40010
European-Finnish (FIN)
AF:
AC:
4113
AN:
26996
Middle Eastern (MID)
AF:
AC:
295
AN:
1810
European-Non Finnish (NFE)
AF:
AC:
43823
AN:
266526
Other (OTH)
AF:
AC:
3915
AN:
23876
⚠️ 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: 0.371
Heterozygous variant carriers
0
3144
6288
9432
12576
15720
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
344
688
1032
1376
1720
<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 0.135 AC: 14913AN: 110176Hom.: 1560 Cov.: 0 AF XY: 0.126 AC XY: 6585AN XY: 52196 show subpopulations
GnomAD4 genome
AF:
AC:
14913
AN:
110176
Hom.:
Cov.:
0
AF XY:
AC XY:
6585
AN XY:
52196
show subpopulations
African (AFR)
AF:
AC:
2879
AN:
32302
American (AMR)
AF:
AC:
1229
AN:
10568
Ashkenazi Jewish (ASJ)
AF:
AC:
566
AN:
2592
East Asian (EAS)
AF:
AC:
541
AN:
3320
South Asian (SAS)
AF:
AC:
223
AN:
3454
European-Finnish (FIN)
AF:
AC:
580
AN:
5756
Middle Eastern (MID)
AF:
AC:
15
AN:
170
European-Non Finnish (NFE)
AF:
AC:
8634
AN:
49932
Other (OTH)
AF:
AC:
178
AN:
1462
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.493
Heterozygous variant carriers
0
431
862
1294
1725
2156
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
142
284
426
568
710
<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:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
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;