3-187729443-G-A
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001706.5(BCL6):c.962C>T(p.Ala321Val) variant causes a missense change. The variant allele was found at a frequency of 0.000217 in 1,609,986 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).
Frequency
Genomes: 𝑓 0.000092 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00023 ( 0 hom. )
Consequence
BCL6
NM_001706.5 missense
NM_001706.5 missense
Scores
6
13
Clinical Significance
Conservation
PhyloP100: 7.13
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.1215646).
BS2
High AC in GnomAd4 at 14 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BCL6 | NM_001706.5 | c.962C>T | p.Ala321Val | missense_variant | 5/10 | ENST00000406870.7 | NP_001697.2 | |
LOC100131635 | NR_034062.1 | n.294-2928G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BCL6 | ENST00000406870.7 | c.962C>T | p.Ala321Val | missense_variant | 5/10 | 1 | NM_001706.5 | ENSP00000384371 | P1 | |
ENST00000449623.5 | n.347-4081G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152104Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000846 AC: 21AN: 248326Hom.: 0 AF XY: 0.000104 AC XY: 14AN XY: 134120
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GnomAD4 exome AF: 0.000230 AC: 335AN: 1457882Hom.: 0 Cov.: 34 AF XY: 0.000219 AC XY: 159AN XY: 724834
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GnomAD4 genome AF: 0.0000920 AC: 14AN: 152104Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74288
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ClinVar
Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link
Submissions by phenotype
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
.;T;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;.;D;.
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N;N;N
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
.;N;N;N
REVEL
Benign
Sift
Benign
.;T;T;T
Sift4G
Benign
T;T;T;T
Polyphen
0.52
.;P;P;.
Vest4
MVP
MPC
0.20
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at