Genetic Variant BCL2L15:n.1178G>A (chr1-113881031-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000369580.3(BCL2L15):n.1178G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 1,581,740 control chromosomes in the GnomAD database, including 91,087 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 0.43 ( 18045 hom., cov: 32)

Exomes 𝑓: 0.31 ( 73042 hom. )

Consequence

BCL2L15
ENST00000369580.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.17

Publications

27 publications found

Variant links:

Genes affected

BCL2L15 (HGNC:33624): (BCL2 like 15) Predicted to be involved in apoptotic process and regulation of apoptotic process. Predicted to be active in cytosol and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

BCL2L15 links:

AP4B1-AS1 (HGNC:44114): (AP4B1 antisense RNA 1)

AP4B1-AS1 links:

Genome browser will be placed here

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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
BCL2L15	NM_001010922.3 link	c.*92G>A	3_prime_UTR_variant	Exon 4 of 4	ENST00000393316.8	NP_001010922.1	Q5TBC7-1Q53EI7
AP4B1-AS1	NR_037864.1 link	n.247-16837C>T	intron_variant	Intron 3 of 4
AP4B1-AS1	NR_125965.1 link	n.415-16837C>T	intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCL2L15	ENST00000393316.8 link	c.*92G>A		3_prime_UTR_variant	Exon 4 of 4	1	NM_001010922.3	ENSP00000376992.3		Q5TBC7-1

Frequencies

GnomAD3 genomes

AF:

0.426

AC:

64719

AN:

151932

Hom.:

17994

Cov.:

show subpopulations

Gnomad AFR

AF:

0.795

Gnomad AMI

AF:

0.344

Gnomad AMR

AF:

0.261

Gnomad ASJ

AF:

0.388

Gnomad EAS

AF:

0.0772

Gnomad SAS

AF:

0.282

Gnomad FIN

AF:

0.259

Gnomad MID

AF:

0.332

Gnomad NFE

AF:

0.306

Gnomad OTH

AF:

0.386

GnomAD4 exome

AF:

0.305

AC:

436714

AN:

1429690

Hom.:

73042

Cov.:

AF XY:

0.304

AC XY:

216624

AN XY:

712652

show subpopulations

African (AFR)

AF:

0.819

AC:

26593

AN:

32482

American (AMR)

AF:

0.179

AC:

7841

AN:

43800

Ashkenazi Jewish (ASJ)

AF:

0.396

AC:

10203

AN:

25736

East Asian (EAS)

AF:

0.0949

AC:

3730

AN:

39320

South Asian (SAS)

AF:

0.297

AC:

25076

AN:

84550

European-Finnish (FIN)

AF:

0.272

AC:

14454

AN:

53230

Middle Eastern (MID)

AF:

0.347

AC:

1980

AN:

5702

European-Non Finnish (NFE)

AF:

0.302

AC:

327458

AN:

1085658

Other (OTH)

AF:

0.327

AC:

19379

AN:

59212

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

13861

27723

41584

55446

69307

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.426

AC:

64824

AN:

152050

Hom.:

18045

Cov.:

AF XY:

0.417

AC XY:

31015

AN XY:

74326

show subpopulations

African (AFR)

AF:

0.795

AC:

32977

AN:

41480

American (AMR)

AF:

0.261

AC:

3979

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.388

AC:

1345

AN:

3468

East Asian (EAS)

AF:

0.0774

AC:

401

AN:

5182

South Asian (SAS)

AF:

0.281

AC:

1357

AN:

4826

European-Finnish (FIN)

AF:

0.259

AC:

2730

AN:

10556

Middle Eastern (MID)

AF:

0.330

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.306

AC:

20816

AN:

67956

Other (OTH)

AF:

0.383

AC:

810

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1502

3004

4507

6009

7511

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.334

Hom.:

25794

Bravo

AF:

0.437

Asia WGS

AF:

0.215

AC:

748

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.096

(source)

DANN

Benign

0.41

PhyloP100

-1.2

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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1-113881031-C-T

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