rs10521149

chr17-7028821-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_181844.4(BCL6B):c.*1202A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0626 in 985,372 control chromosomes in the GnomAD database, including 1,927 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 0.054 (234 hom., cov: 33)
  • Exomes 𝑓: 0.064 (1693 hom.)
• Consequence: BCL6B NM_181844.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.557

Genes affected

BCL6B (HGNC:1002): (BCL6B transcription repressor) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in several processes, including regulation of gene expression; regulation of inflammatory response; and type 2 immune response. Predicted to be located in nucleus. Predicted to be active in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCL6B	NM_181844.4	c.*1202A>C		3_prime_UTR_variant	9/9	ENST00000293805.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCL6B	ENST00000293805.10	c.*1202A>C		3_prime_UTR_variant	9/9	1	NM_181844.4	P1
BCL6B	ENST00000537931.2	c.391-995A>C		intron_variant		3
BCL6B	ENST00000571729.1	n.298-995A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0543 AC: 8257 AN: 152160 Hom.: 235 Cov.: 33

Gnomad AFR AF: 0.0500

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0388

Gnomad ASJ AF: 0.0429

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0348

Gnomad FIN AF: 0.0530

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0666

Gnomad OTH AF: 0.0613

GnomAD4 exome AF: 0.0641 AC: 53439 AN: 833094 Hom.: 1693 Cov.: 33 AF XY: 0.0643 AC XY: 24727 AN XY: 384710

Gnomad4 AFR exome AF: 0.0526

Gnomad4 AMR exome AF: 0.0427

Gnomad4 ASJ exome AF: 0.0532

Gnomad4 EAS exome AF: 0.000275

Gnomad4 SAS exome AF: 0.0396

Gnomad4 FIN exome AF: 0.0870

Gnomad4 NFE exome AF: 0.0656

Gnomad4 OTH exome AF: 0.0545

GnomAD4 genome AF: 0.0542 AC: 8259 AN: 152278 Hom.: 234 Cov.: 33 AF XY: 0.0528 AC XY: 3933 AN XY: 74462

Gnomad4 AFR AF: 0.0500

Gnomad4 AMR AF: 0.0388

Gnomad4 ASJ AF: 0.0429

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0348

Gnomad4 FIN AF: 0.0530

Gnomad4 NFE AF: 0.0666

Gnomad4 OTH AF: 0.0607

Alfa AF: 0.0648 Hom.: 449

Bravo AF: 0.0543

Asia WGS AF: 0.0250 AC: 89 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	5.3
Dann	Benign	0.41

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

Other links and lift over

dbSNP: rs10521149; hg19: chr17-6932140;