rs1056932

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001706.5(BCL6):​c.1161C>T​(p.Asn387Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 1,613,920 control chromosomes in the GnomAD database, including 341,613 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.54 ( 25905 hom., cov: 31)
Exomes 𝑓: 0.65 ( 315708 hom. )

Consequence

BCL6
NM_001706.5 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.773
Variant links:
Genes affected
BCL6 (HGNC:1001): (BCL6 transcription repressor) The protein encoded by this gene is a zinc finger transcription factor and contains an N-terminal POZ domain. This protein acts as a sequence-specific repressor of transcription, and has been shown to modulate the transcription of STAT-dependent IL-4 responses of B cells. This protein can interact with a variety of POZ-containing proteins that function as transcription corepressors. This gene is found to be frequently translocated and hypermutated in diffuse large-cell lymphoma (DLCL), and may be involved in the pathogenesis of DLCL. Alternatively spliced transcript variants encoding different protein isoforms have been found for this gene. [provided by RefSeq, Aug 2015]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BP7
Synonymous conserved (PhyloP=0.773 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
BCL6NM_001706.5 linkc.1161C>T p.Asn387Asn synonymous_variant Exon 5 of 10 ENST00000406870.7 NP_001697.2 P41182-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
BCL6ENST00000406870.7 linkc.1161C>T p.Asn387Asn synonymous_variant Exon 5 of 10 1 NM_001706.5 ENSP00000384371.2 P41182-1

Frequencies

GnomAD3 genomes
AF:
0.539
AC:
81937
AN:
151936
Hom.:
25893
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.184
Gnomad AMI
AF:
0.802
Gnomad AMR
AF:
0.701
Gnomad ASJ
AF:
0.710
Gnomad EAS
AF:
0.798
Gnomad SAS
AF:
0.653
Gnomad FIN
AF:
0.701
Gnomad MID
AF:
0.731
Gnomad NFE
AF:
0.652
Gnomad OTH
AF:
0.596
GnomAD2 exomes
AF:
0.658
AC:
165326
AN:
251440
AF XY:
0.661
show subpopulations
Gnomad AFR exome
AF:
0.169
Gnomad AMR exome
AF:
0.776
Gnomad ASJ exome
AF:
0.702
Gnomad EAS exome
AF:
0.797
Gnomad FIN exome
AF:
0.694
Gnomad NFE exome
AF:
0.659
Gnomad OTH exome
AF:
0.676
GnomAD4 exome
AF:
0.651
AC:
951884
AN:
1461866
Hom.:
315708
Cov.:
88
AF XY:
0.652
AC XY:
474009
AN XY:
727232
show subpopulations
Gnomad4 AFR exome
AF:
0.160
AC:
5344
AN:
33480
Gnomad4 AMR exome
AF:
0.769
AC:
34409
AN:
44724
Gnomad4 ASJ exome
AF:
0.702
AC:
18360
AN:
26136
Gnomad4 EAS exome
AF:
0.824
AC:
32727
AN:
39700
Gnomad4 SAS exome
AF:
0.646
AC:
55701
AN:
86258
Gnomad4 FIN exome
AF:
0.690
AC:
36830
AN:
53404
Gnomad4 NFE exome
AF:
0.652
AC:
725547
AN:
1112002
Gnomad4 Remaining exome
AF:
0.645
AC:
38962
AN:
60396
Heterozygous variant carriers
0
22876
45752
68628
91504
114380
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Exome Het
Exome Hom
Variant carriers
0
18908
37816
56724
75632
94540
<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:
0.539
AC:
81972
AN:
152054
Hom.:
25905
Cov.:
31
AF XY:
0.549
AC XY:
40771
AN XY:
74304
show subpopulations
Gnomad4 AFR
AF:
0.184
AC:
0.183918
AN:
0.183918
Gnomad4 AMR
AF:
0.702
AC:
0.701569
AN:
0.701569
Gnomad4 ASJ
AF:
0.710
AC:
0.709919
AN:
0.709919
Gnomad4 EAS
AF:
0.799
AC:
0.799182
AN:
0.799182
Gnomad4 SAS
AF:
0.655
AC:
0.655338
AN:
0.655338
Gnomad4 FIN
AF:
0.701
AC:
0.701437
AN:
0.701437
Gnomad4 NFE
AF:
0.652
AC:
0.651615
AN:
0.651615
Gnomad4 OTH
AF:
0.597
AC:
0.597156
AN:
0.597156
Heterozygous variant carriers
0
1575
3150
4725
6300
7875
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
686
1372
2058
2744
3430
<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:
0.616
Hom.:
50120
Bravo
AF:
0.525
Asia WGS
AF:
0.669
AC:
2327
AN:
3478
EpiCase
AF:
0.666
EpiControl
AF:
0.669

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.61
CADD
Benign
5.9
DANN
Benign
0.84
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Mutation Taster
=91/9
polymorphism (auto)

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1056932; hg19: chr3-187447032; COSMIC: COSV51649553; COSMIC: COSV51649553; API