rs1474326
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001706.5(BCL6):c.1977+202G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 691,196 control chromosomes in the GnomAD database, including 67,281 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 0.36 ( 11915 hom., cov: 32)
Exomes 𝑓: 0.44 ( 55366 hom. )
Consequence
BCL6
NM_001706.5 intron
NM_001706.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.237
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 Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCL6 | NM_001706.5 | c.1977+202G>T | intron_variant | ENST00000406870.7 | |||
LOC100131635 | NR_034062.1 | n.294-7632C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCL6 | ENST00000406870.7 | c.1977+202G>T | intron_variant | 1 | NM_001706.5 | P1 | |||
ENST00000449623.5 | n.347-8785C>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.357 AC: 54191AN: 151966Hom.: 11913 Cov.: 32
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GnomAD4 exome AF: 0.444 AC: 239157AN: 539112Hom.: 55366 Cov.: 7 AF XY: 0.438 AC XY: 122209AN XY: 278794
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GnomAD4 genome ? AF: 0.356 AC: 54192AN: 152084Hom.: 11915 Cov.: 32 AF XY: 0.361 AC XY: 26860AN XY: 74314
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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