Genetic Variant BCL2L15:n.3518G>A (chr1-113878691-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000369580.3(BCL2L15):n.3518G>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 0.216 in 152,228 control chromosomes in the GnomAD database, including 4,529 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 0.22 ( 4523 hom., cov: 32)

Exomes 𝑓: 0.31 ( 6 hom. )

Consequence

BCL2L15
ENST00000369580.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.41

Publications

16 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 -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.25).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
BCL2L15	NM_001010922.3 link	c.*2432G>A	3_prime_UTR_variant	Exon 4 of 4	ENST00000393316.8	NP_001010922.1	Q5TBC7-1Q53EI7
AP4B1-AS1	NR_037864.1 link	n.247-19177C>T	intron_variant	Intron 3 of 4
AP4B1-AS1	NR_125965.1 link	n.415-19177C>T	intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
BCL2L15	ENST00000369580.3 link	n.3518G>A	non_coding_transcript_exon_variant	Exon 2 of 2	1
BCL2L15	ENST00000393316.8 link	c.*2432G>A	3_prime_UTR_variant	Exon 4 of 4	1	NM_001010922.3	ENSP00000376992.3	Q5TBC7-1
AP4B1-AS1	ENST00000419536.1 link	n.247-19177C>T	intron_variant	Intron 3 of 4	2
AP4B1-AS1	ENST00000717022.1 link	n.441-16469C>T	intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes

AF:

0.217

AC:

32916

AN:

151976

Hom.:

4529

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0852

Gnomad AMI

AF:

0.164

Gnomad AMR

AF:

0.346

Gnomad ASJ

AF:

0.224

Gnomad EAS

AF:

0.619

Gnomad SAS

AF:

0.217

Gnomad FIN

AF:

0.301

Gnomad MID

AF:

0.266

Gnomad NFE

AF:

0.223

Gnomad OTH

AF:

0.241

GnomAD4 exome

AF:

0.306

AC:

AN:

134

Hom.:

Cov.:

AF XY:

0.278

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.306

AC:

AN:

134

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.216

AC:

32907

AN:

152094

Hom.:

4523

Cov.:

AF XY:

0.224

AC XY:

16656

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.0849

AC:

3526

AN:

41532

American (AMR)

AF:

0.346

AC:

5289

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.224

AC:

778

AN:

3470

East Asian (EAS)

AF:

0.619

AC:

3198

AN:

5170

South Asian (SAS)

AF:

0.217

AC:

1045

AN:

4822

European-Finnish (FIN)

AF:

0.301

AC:

3173

AN:

10532

Middle Eastern (MID)

AF:

0.255

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.223

AC:

15168

AN:

67968

Other (OTH)

AF:

0.240

AC:

505

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1232

2464

3695

4927

6159

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

360

720

1080

1440

1800

<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:

0.228

Hom.:

6867

Bravo

AF:

0.222

Asia WGS

AF:

0.345

AC:

1198

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.25

CADD

Benign

7.1

(source)

DANN

Benign

0.73

PhyloP100

1.4

Splicing

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