Variant rs4488761 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_015367.4(BCL2L13):c.771A>G(p.Ser257Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 1,613,882 control chromosomes in the GnomAD database, including 254,484 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 0.57 ( 25690 hom., cov: 32)

Exomes 𝑓: 0.55 ( 228794 hom. )

Consequence

BCL2L13
NM_015367.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.629

Variant links:

Genes affected

BCL2L13 (HGNC:17164): (BCL2 like 13) This gene encodes a mitochondrially-localized protein with conserved B-cell lymphoma 2 homology motifs. Overexpression of the encoded protein results in apoptosis. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Jul 2012]

BCL2L13 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP7

Synonymous conserved (PhyloP=-0.629 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BCL2L13	NM_015367.4 link	c.771A>G	p.Ser257Ser	synonymous_variant	7/7	ENST00000317582.10	NP_056182.2	Q9BXK5-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BCL2L13	ENST00000317582.10 link	c.771A>G	p.Ser257Ser	synonymous_variant	7/7	1	NM_015367.4	ENSP00000318883.5		Q9BXK5-1

Frequencies

GnomAD3 genomes

AF:

0.573

AC:

87139

AN:

151958

Hom.:

25673

Cov.:

show subpopulations

Gnomad AFR

AF:

0.600

Gnomad AMI

AF:

0.604

Gnomad AMR

AF:

0.639

Gnomad ASJ

AF:

0.582

Gnomad EAS

AF:

0.927

Gnomad SAS

AF:

0.645

Gnomad FIN

AF:

0.507

Gnomad MID

AF:

0.513

Gnomad NFE

AF:

0.521

Gnomad OTH

AF:

0.560

GnomAD3 exomes

AF:

0.596

AC:

149588

AN:

251064

Hom.:

46227

AF XY:

0.591

AC XY:

80179

AN XY:

135708

show subpopulations

Gnomad AFR exome

AF:

0.603

Gnomad AMR exome

AF:

0.682

Gnomad ASJ exome

AF:

0.581

Gnomad EAS exome

AF:

0.927

Gnomad SAS exome

AF:

0.639

Gnomad FIN exome

AF:

0.510

Gnomad NFE exome

AF:

0.522

Gnomad OTH exome

AF:

0.575

GnomAD4 exome

AF:

0.553

AC:

808425

AN:

1461806

Hom.:

228794

Cov.:

AF XY:

0.555

AC XY:

403283

AN XY:

727202

show subpopulations

Gnomad4 AFR exome

AF:

0.597

Gnomad4 AMR exome

AF:

0.678

Gnomad4 ASJ exome

AF:

0.585

Gnomad4 EAS exome

AF:

0.949

Gnomad4 SAS exome

AF:

0.636

Gnomad4 FIN exome

AF:

0.502

Gnomad4 NFE exome

AF:

0.527

Gnomad4 OTH exome

AF:

0.570

GnomAD4 genome

AF:

0.573

AC:

87208

AN:

152076

Hom.:

25690

Cov.:

AF XY:

0.577

AC XY:

42932

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.600

Gnomad4 AMR

AF:

0.640

Gnomad4 ASJ

AF:

0.582

Gnomad4 EAS

AF:

0.926

Gnomad4 SAS

AF:

0.644

Gnomad4 FIN

AF:

0.507

Gnomad4 NFE

AF:

0.521

Gnomad4 OTH

AF:

0.563

Alfa

AF:

0.540

Hom.:

33797

Bravo

AF:

0.587

Asia WGS

AF:

0.764

AC:

2657

AN:

3478

EpiCase

AF:

0.528

EpiControl

AF:

0.530

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

0.81

DANN

Benign

0.63

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