Variant rs1564483 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000333681.5(BCL2):c.*1204G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 235,960 control chromosomes in the GnomAD database, including 6,861 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 0.22 ( 4179 hom., cov: 32)

Exomes 𝑓: 0.25 ( 2682 hom. )

Consequence

BCL2
ENST00000333681.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.29

Variant links:

Genes affected

BCL2 (HGNC:990): (BCL2 apoptosis regulator) This gene encodes an integral outer mitochondrial membrane protein that blocks the apoptotic death of some cells such as lymphocytes. Constitutive expression of BCL2, such as in the case of translocation of BCL2 to Ig heavy chain locus, is thought to be the cause of follicular lymphoma. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]

BCL2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BCL2	NM_000633.3 linkuse as main transcript	c.*1204G>A		3_prime_UTR_variant	3/3	ENST00000333681.5	NP_000624.2
BCL2	XM_047437733.1 linkuse as main transcript	c.*1204G>A		3_prime_UTR_variant	2/2		XP_047293689.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BCL2	ENST00000333681.5 linkuse as main transcript	c.*1204G>A		3_prime_UTR_variant	3/3	1	NM_000633.3	ENSP00000329623	P1	P10415-1

Frequencies

GnomAD3 genomes

AF:

0.220

AC:

33524

AN:

152064

Hom.:

4181

Cov.:

show subpopulations

Gnomad AFR

AF:

0.118

Gnomad AMI

AF:

0.285

Gnomad AMR

AF:

0.163

Gnomad ASJ

AF:

0.209

Gnomad EAS

AF:

0.380

Gnomad SAS

AF:

0.228

Gnomad FIN

AF:

0.294

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.272

Gnomad OTH

AF:

0.209

GnomAD4 exome

AF:

0.249

AC:

20857

AN:

83778

Hom.:

2682

Cov.:

AF XY:

0.250

AC XY:

9712

AN XY:

38894

show subpopulations

Gnomad4 AFR exome

AF:

0.108

Gnomad4 AMR exome

AF:

0.153

Gnomad4 ASJ exome

AF:

0.220

Gnomad4 EAS exome

AF:

0.292

Gnomad4 SAS exome

AF:

0.213

Gnomad4 FIN exome

AF:

0.251

Gnomad4 NFE exome

AF:

0.260

Gnomad4 OTH exome

AF:

0.230

GnomAD4 genome

AF:

0.220

AC:

33518

AN:

152182

Hom.:

4179

Cov.:

AF XY:

0.220

AC XY:

16399

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.118

Gnomad4 AMR

AF:

0.163

Gnomad4 ASJ

AF:

0.209

Gnomad4 EAS

AF:

0.380

Gnomad4 SAS

AF:

0.228

Gnomad4 FIN

AF:

0.294

Gnomad4 NFE

AF:

0.272

Gnomad4 OTH

AF:

0.208

Alfa

AF:

0.254

Hom.:

6953

Bravo

AF:

0.205

Asia WGS

AF:

0.270

AC:

940

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.047

DANN

Benign

0.62

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over