dbSNP rs4488761: BCL2L13:p.Ser257Ser (chr22-17726847-A-G) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

33 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
BCL2L13	NM_015367.4 link	c.771A>G	p.Ser257Ser	synonymous_variant	Exon 7 of 7	ENST00000317582.10	NP_056182.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCL2L13	ENST00000317582.10 link	c.771A>G	p.Ser257Ser	synonymous_variant	Exon 7 of 7	1	NM_015367.4	ENSP00000318883.5

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

GnomAD2 exomes

AF:

0.596

AC:

149588

AN:

251064

AF XY:

0.591

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 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

African (AFR)

AF:

0.597

AC:

20002

AN:

33480

American (AMR)

AF:

0.678

AC:

30328

AN:

44706

Ashkenazi Jewish (ASJ)

AF:

0.585

AC:

15291

AN:

26134

East Asian (EAS)

AF:

0.949

AC:

37659

AN:

39700

South Asian (SAS)

AF:

0.636

AC:

54852

AN:

86258

European-Finnish (FIN)

AF:

0.502

AC:

26813

AN:

53412

Middle Eastern (MID)

AF:

0.582

AC:

3358

AN:

5768

European-Non Finnish (NFE)

AF:

0.527

AC:

585693

AN:

1111954

Other (OTH)

AF:

0.570

AC:

34429

AN:

60394

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

22965

45929

68894

91858

114823

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17070

34140

51210

68280

85350

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.573

AC:

87208

AN:

152076

Hom.:

25690

Cov.:

AF XY:

0.577

AC XY:

42932

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.600

AC:

24864

AN:

41464

American (AMR)

AF:

0.640

AC:

9783

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.582

AC:

2020

AN:

3472

East Asian (EAS)

AF:

0.926

AC:

4793

AN:

5176

South Asian (SAS)

AF:

0.644

AC:

3109

AN:

4826

European-Finnish (FIN)

AF:

0.507

AC:

5351

AN:

10560

Middle Eastern (MID)

AF:

0.497

AC:

146

AN:

294

European-Non Finnish (NFE)

AF:

0.521

AC:

35403

AN:

67970

Other (OTH)

AF:

0.563

AC:

1188

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1876

3752

5627

7503

9379

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

732

1464

2196

2928

3660

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.544

Hom.:

42387

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

(source)

DANN

Benign

0.63

PhyloP100

-0.63

Mutation Taster

=95/5

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over