Genetic Variant BCL2L13:n.*1861T>C (chr22-17728439-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000399777.2(BCL2L13):n.*1861T>C 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 0.454 in 152,132 control chromosomes in the GnomAD database, including 16,545 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 0.45 ( 16545 hom., cov: 32)

Exomes 𝑓: 0.25 ( 0 hom. )

Consequence

BCL2L13
ENST00000399777.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.32

Publications

18 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000399777.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
BCL2L13	NM_015367.4	MANE Select	c.*905T>C	3_prime_UTR	Exon 7 of 7	NP_056182.2
BCL2L13	NR_073068.1		n.2314T>C	non_coding_transcript_exon	Exon 5 of 5
BCL2L13	NR_073069.1		n.2297T>C	non_coding_transcript_exon	Exon 5 of 5

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
BCL2L13	ENST00000399777.2	TSL:1	n.*1861T>C	non_coding_transcript_exon	Exon 6 of 6	ENSP00000382677.2
BCL2L13	ENST00000317582.10	TSL:1 MANE Select	c.*905T>C	3_prime_UTR	Exon 7 of 7	ENSP00000318883.5
BCL2L13	ENST00000355028.4	TSL:1	c.*1633T>C	3_prime_UTR	Exon 5 of 5	ENSP00000347133.3

Frequencies

GnomAD3 genomes

AF:

0.454

AC:

69007

AN:

152006

Hom.:

16542

Cov.:

show subpopulations

Gnomad AFR

AF:

0.360

Gnomad AMI

AF:

0.583

Gnomad AMR

AF:

0.562

Gnomad ASJ

AF:

0.457

Gnomad EAS

AF:

0.813

Gnomad SAS

AF:

0.592

Gnomad FIN

AF:

0.462

Gnomad MID

AF:

0.427

Gnomad NFE

AF:

0.447

Gnomad OTH

AF:

0.459

GnomAD4 exome

AF:

0.250

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.250

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.625

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.454

AC:

69041

AN:

152124

Hom.:

16545

Cov.:

AF XY:

0.462

AC XY:

34326

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.359

AC:

14908

AN:

41490

American (AMR)

AF:

0.563

AC:

8603

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.457

AC:

1586

AN:

3472

East Asian (EAS)

AF:

0.812

AC:

4206

AN:

5178

South Asian (SAS)

AF:

0.591

AC:

2853

AN:

4824

European-Finnish (FIN)

AF:

0.462

AC:

4895

AN:

10584

Middle Eastern (MID)

AF:

0.415

AC:

122

AN:

294

European-Non Finnish (NFE)

AF:

0.447

AC:

30361

AN:

67976

Other (OTH)

AF:

0.462

AC:

975

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1889

3777

5666

7554

9443

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

632

1264

1896

2528

3160

<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:

0.458

Hom.:

24177

Bravo

AF:

0.462

Asia WGS

AF:

0.667

AC:

2315

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.47

(source)

DANN

Benign

0.52

PhyloP100

-1.3

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over