rs16862537

Variant names:

• chr3-187746184-T-C
• rs16862537
• ENST00000793818.1:n.314+2140T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000793818.1(BCL6-AS1):​n.314+2140T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 151,962 control chromosomes in the GnomAD database, including 3,782 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 0.20 (3782 hom., cov: 31)
• Consequence: BCL6-AS1 ENST00000793818.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 3 publications found

Genes affected

BCL6-AS1 (HGNC:):

BCL6-AS1 (HGNC:51843): (BCL6 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000793818.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCL6-AS1	NR_173091.1		n.*158T>C		downstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCL6-AS1	ENST00000793818.1		n.314+2140T>C		intron	N/A
	BCL6-AS1	ENST00000793819.1		n.77+225T>C		intron	N/A
	BCL6-AS1	ENST00000793820.1		n.193+100T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30453 AN: 151842 Hom.: 3785 Cov.: 31

Gnomad AFR AF: 0.0586

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.230

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.200 AC: 30438 AN: 151962 Hom.: 3782 Cov.: 31 AF XY: 0.197 AC XY: 14613 AN XY: 74274

African (AFR) AF: 0.0585 AC: 2425 AN: 41488

American (AMR) AF: 0.212 AC: 3230 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1235 AN: 3462

East Asian (EAS) AF: 0.208 AC: 1074 AN: 5158

South Asian (SAS) AF: 0.262 AC: 1258 AN: 4810

European-Finnish (FIN) AF: 0.163 AC: 1727 AN: 10566

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.276 AC: 18716 AN: 67934

Other (OTH) AF: 0.228 AC: 479 AN: 2098

Alfa AF: 0.206 Hom.: 546

Bravo AF: 0.196

Asia WGS AF: 0.206 AC: 719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	14
DANN	Benign	0.74
PhyloP100		1.0
PromoterAI		-0.0032	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs16862537;

hg19: chr3-187463972;

COSMIC: COSV69206459;