dbSNP rs2448050: BCL2L14:c.945+1360G>A (chr12-12096290-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_138723.2(BCL2L14):c.945+1360G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 522,798 control chromosomes in the GnomAD database, including 81,399 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 0.51 ( 20311 hom., cov: 31)

Exomes 𝑓: 0.57 ( 61088 hom. )

Consequence

BCL2L14
NM_138723.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.651

Publications

7 publications found

Variant links:

Genes affected

BCL2L14 (HGNC:16657): (BCL2 like 14) The protein encoded by this gene belongs to the BCL2 protein family. BCL2 family members form hetero- or homodimers and act as anti- or pro-apoptotic regulators that are involved in a wide variety of cellular activities. Overexpression of this gene has been shown to induce apoptosis in cells. Three alternatively spliced transcript variants encoding two distinct isoforms have been reported for this gene. [provided by RefSeq, May 2009]

BCL2L14 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCL2L14	NM_138723.2 link	c.945+1360G>A		intron_variant	Intron 5 of 5	ENST00000308721.9	NP_620049.1	Q9BZR8-1A0A024RAR1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCL2L14	ENST00000308721.9 link	c.945+1360G>A		intron_variant	Intron 5 of 5	1	NM_138723.2	ENSP00000309132.4		Q9BZR8-1

Frequencies

GnomAD3 genomes

AF:

0.510

AC:

77307

AN:

151654

Hom.:

20309

Cov.:

show subpopulations

Gnomad AFR

AF:

0.381

Gnomad AMI

AF:

0.538

Gnomad AMR

AF:

0.488

Gnomad ASJ

AF:

0.505

Gnomad EAS

AF:

0.652

Gnomad SAS

AF:

0.593

Gnomad FIN

AF:

0.546

Gnomad MID

AF:

0.465

Gnomad NFE

AF:

0.571

Gnomad OTH

AF:

0.497

GnomAD4 exome

AF:

0.573

AC:

212714

AN:

371026

Hom.:

61088

AF XY:

0.573

AC XY:

100505

AN XY:

175278

show subpopulations

African (AFR)

AF:

0.352

AC:

2344

AN:

6664

American (AMR)

AF:

0.495

AC:

210

AN:

424

Ashkenazi Jewish (ASJ)

AF:

0.520

AC:

1234

AN:

2374

East Asian (EAS)

AF:

0.643

AC:

987

AN:

1536

South Asian (SAS)

AF:

0.577

AC:

4157

AN:

7210

European-Finnish (FIN)

AF:

0.524

AC:

AN:

124

Middle Eastern (MID)

AF:

0.435

AC:

317

AN:

728

European-Non Finnish (NFE)

AF:

0.578

AC:

196583

AN:

339954

Other (OTH)

AF:

0.568

AC:

6817

AN:

12012

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

4423

8846

13270

17693

22116

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7380

14760

22140

29520

36900

<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:

0.510

AC:

77336

AN:

151772

Hom.:

20311

Cov.:

AF XY:

0.509

AC XY:

37744

AN XY:

74176

show subpopulations

African (AFR)

AF:

0.380

AC:

15726

AN:

41342

American (AMR)

AF:

0.488

AC:

7447

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.505

AC:

1752

AN:

3470

East Asian (EAS)

AF:

0.653

AC:

3371

AN:

5166

South Asian (SAS)

AF:

0.592

AC:

2835

AN:

4792

European-Finnish (FIN)

AF:

0.546

AC:

5729

AN:

10500

Middle Eastern (MID)

AF:

0.459

AC:

135

AN:

294

European-Non Finnish (NFE)

AF:

0.571

AC:

38806

AN:

67940

Other (OTH)

AF:

0.495

AC:

1044

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1900

3800

5700

7600

9500

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

694

1388

2082

2776

3470

<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:

0.549

Hom.:

99270

Bravo

AF:

0.499

Asia WGS

AF:

0.555

AC:

1930

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.46

(source)

DANN

Benign

0.74

PhyloP100

-0.65

Mutation Taster

=100/0

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