Variant rs4987845 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_000633.3(BCL2):c.*670G>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 0.0633 in 225,312 control chromosomes in the GnomAD database, including 605 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 0.059 ( 369 hom., cov: 33)

Exomes 𝑓: 0.072 ( 236 hom. )

Consequence

BCL2
NM_000633.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.673

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=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0906 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.*670G>A		3_prime_UTR_variant	3/3	ENST00000333681.5	NP_000624.2
BCL2	XM_047437733.1 linkuse as main transcript	c.*670G>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.*670G>A		3_prime_UTR_variant	3/3	1	NM_000633.3	ENSP00000329623	P1	P10415-1

Frequencies

GnomAD3 genomes

AF:

0.0593

AC:

9025

AN:

152152

Hom.:

369

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0162

Gnomad AMI

AF:

0.0548

Gnomad AMR

AF:

0.0635

Gnomad ASJ

AF:

0.0668

Gnomad EAS

AF:

0.000576

Gnomad SAS

AF:

0.0230

Gnomad FIN

AF:

0.0478

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.0926

Gnomad OTH

AF:

0.0765

GnomAD4 exome

AF:

0.0718

AC:

5244

AN:

73042

Hom.:

236

Cov.:

AF XY:

0.0727

AC XY:

2455

AN XY:

33790

show subpopulations

Gnomad4 AFR exome

AF:

0.0193

Gnomad4 AMR exome

AF:

0.0511

Gnomad4 ASJ exome

AF:

0.0659

Gnomad4 EAS exome

AF:

0.00133

Gnomad4 SAS exome

AF:

0.0180

Gnomad4 FIN exome

AF:

0.0360

Gnomad4 NFE exome

AF:

0.0941

Gnomad4 OTH exome

AF:

0.0763

GnomAD4 genome

AF:

0.0593

AC:

9027

AN:

152270

Hom.:

369

Cov.:

AF XY:

0.0570

AC XY:

4242

AN XY:

74460

show subpopulations

Gnomad4 AFR

AF:

0.0162

Gnomad4 AMR

AF:

0.0635

Gnomad4 ASJ

AF:

0.0668

Gnomad4 EAS

AF:

0.000578

Gnomad4 SAS

AF:

0.0230

Gnomad4 FIN

AF:

0.0478

Gnomad4 NFE

AF:

0.0926

Gnomad4 OTH

AF:

0.0776

Alfa

AF:

0.0858

Hom.:

586

Bravo

AF:

0.0597

Asia WGS

AF:

0.0250

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

2.6

DANN

Benign

0.69

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