dbSNP rs737993: BCL2L13:c.-650+82C>A (chr22-17629087-C-A) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000399782.5(BCL2L13):c.-650+82C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0755 in 158,326 control chromosomes in the GnomAD database, including 538 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.077 ( 530 hom., cov: 32)

Exomes 𝑓: 0.042 ( 8 hom. )

Consequence

BCL2L13
ENST00000399782.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.618

Publications

0 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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BP6

Variant 22-17629087-C-A is Benign according to our data. Variant chr22-17629087-C-A is described in ClinVar as Benign. ClinVar VariationId is 1274797.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein	UniProt
BCL2L13	XM_011546119.2 link	c.-593+181C>A	intron_variant	Intron 1 of 6	XP_011544421.1	A0A087WX97
BCL2L13	XM_011546120.2 link	c.-593+153C>A	intron_variant	Intron 1 of 6	XP_011544422.1	A0A087WX97
BCL2L13	XM_047441286.1 link	c.-593+82C>A	intron_variant	Intron 1 of 6	XP_047297242.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCL2L13	ENST00000399782.5 link	c.-650+82C>A		intron_variant	Intron 1 of 6	1		ENSP00000382682.1		Q9BXK5-2
BCL2L13	ENST00000399781.5 link	n.52+181C>A		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes

AF:

0.0768

AC:

11674

AN:

151944

Hom.:

530

Cov.:

show subpopulations

Gnomad AFR

AF:

0.115

Gnomad AMI

AF:

0.0625

Gnomad AMR

AF:

0.0442

Gnomad ASJ

AF:

0.0354

Gnomad EAS

AF:

0.000580

Gnomad SAS

AF:

0.0280

Gnomad FIN

AF:

0.0631

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.0747

Gnomad OTH

AF:

0.0707

GnomAD4 exome

AF:

0.0423

AC:

265

AN:

6264

Hom.:

AF XY:

0.0383

AC XY:

140

AN XY:

3660

show subpopulations

African (AFR)

AF:

0.0882

AC:

AN:

170

American (AMR)

AF:

0.0293

AC:

AN:

990

Ashkenazi Jewish (ASJ)

AF:

0.0395

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

366

South Asian (SAS)

AF:

0.0332

AC:

AN:

1596

European-Finnish (FIN)

AF:

0.0488

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0565

AC:

154

AN:

2728

Other (OTH)

AF:

0.0285

AC:

AN:

246

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:

0.0768

AC:

11685

AN:

152062

Hom.:

530

Cov.:

AF XY:

0.0733

AC XY:

5448

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.115

AC:

4781

AN:

41462

American (AMR)

AF:

0.0440

AC:

671

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.0354

AC:

123

AN:

3470

East Asian (EAS)

AF:

0.000581

AC:

AN:

5162

South Asian (SAS)

AF:

0.0276

AC:

133

AN:

4818

European-Finnish (FIN)

AF:

0.0631

AC:

668

AN:

10580

Middle Eastern (MID)

AF:

0.0612

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0748

AC:

5083

AN:

67994

Other (OTH)

AF:

0.0700

AC:

148

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

534

1067

1601

2134

2668

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

256

384

512

640

<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:

0.0294

Hom.:

Bravo

AF:

0.0778

Asia WGS

AF:

0.0200

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Sep 11, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

3.0

(source)

DANN

Benign

0.83

PhyloP100

0.62

PromoterAI

-0.015

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over