Variant rs3210043 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_004050.5(BCL2L2):c.*1703C>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 0.144 in 1,136,690 control chromosomes in the GnomAD database, including 12,985 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 0.11 ( 1198 hom., cov: 32)

Exomes 𝑓: 0.15 ( 11787 hom. )

Consequence

BCL2L2
NM_004050.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.30

Variant links:

Genes affected

BCL2L2 (HGNC:995): (BCL2 like 2) This gene encodes a member of the BCL-2 protein family. The proteins of this family form hetero- or homodimers and act as anti- and pro-apoptotic regulators. Expression of this gene in cells has been shown to contribute to reduced cell apoptosis under cytotoxic conditions. Studies of the related gene in mice indicated a role in the survival of NGF- and BDNF-dependent neurons. Mutation and knockout studies of the mouse gene demonstrated an essential role in adult spermatogenesis. Alternative splicing results in multiple transcript variants. Read-through transcription also exists between this gene and the neighboring downstream PABPN1 (poly(A) binding protein, nuclear 1) gene. [provided by RefSeq, Dec 2010]

BCL2L2 links:

BCL2L2-PABPN1 (HGNC:42959): (BCL2L2-PABPN1 readthrough) This locus represents naturally occurring read-through transcription between the neighboring BCL2L2 (BCL2-like 2) and PABPN1 (poly(A) binding protein, nuclear 1) genes on chromosome 14. The read-through transcript encodes a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Dec 2010]

BCL2L2-PABPN1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.31).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BCL2L2	NM_004050.5 linkuse as main transcript	c.*1703C>A		3_prime_UTR_variant	4/4	ENST00000250405.10	NP_004041.2	Q92843-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BCL2L2	ENST00000250405.10 linkuse as main transcript	c.*1703C>A		3_prime_UTR_variant	4/4	1	NM_004050.5	ENSP00000250405.6		Q92843-1
BCL2L2-PABPN1	ENST00000678502.1 linkuse as main transcript	c.432+2469C>A		intron_variant				ENSP00000503309.1		A0A7I2V383

Frequencies

GnomAD3 genomes

AF:

0.110

AC:

16750

AN:

152034

Hom.:

1193

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0313

Gnomad AMI

AF:

0.105

Gnomad AMR

AF:

0.125

Gnomad ASJ

AF:

0.156

Gnomad EAS

AF:

0.0623

Gnomad SAS

AF:

0.0363

Gnomad FIN

AF:

0.144

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.156

Gnomad OTH

AF:

0.131

GnomAD4 exome

AF:

0.149

AC:

146979

AN:

984538

Hom.:

11787

Cov.:

AF XY:

0.147

AC XY:

68581

AN XY:

467886

show subpopulations

Gnomad4 AFR exome

AF:

0.0196

Gnomad4 AMR exome

AF:

0.121

Gnomad4 ASJ exome

AF:

0.149

Gnomad4 EAS exome

AF:

0.0549

Gnomad4 SAS exome

AF:

0.0370

Gnomad4 FIN exome

AF:

0.130

Gnomad4 NFE exome

AF:

0.161

Gnomad4 OTH exome

AF:

0.126

GnomAD4 genome

AF:

0.110

AC:

16760

AN:

152152

Hom.:

1198

Cov.:

AF XY:

0.107

AC XY:

7991

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.0312

Gnomad4 AMR

AF:

0.124

Gnomad4 ASJ

AF:

0.156

Gnomad4 EAS

AF:

0.0624

Gnomad4 SAS

AF:

0.0363

Gnomad4 FIN

AF:

0.144

Gnomad4 NFE

AF:

0.156

Gnomad4 OTH

AF:

0.135

Alfa

AF:

0.150

Hom.:

1734

Bravo

AF:

0.108

Asia WGS

AF:

0.0610

AC:

211

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.31

CADD

Benign

DANN

Benign

0.89

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