dbSNP rs2516564: CIDEB:c.-414-607G>A (chr14-24309437-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 ENST00000258807.5(CIDEB):c.-414-607G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,200 control chromosomes in the GnomAD database, including 2,932 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 0.18 ( 2932 hom., cov: 32)

Exomes 𝑓: 0.15 ( 0 hom. )

Consequence

CIDEB
ENST00000258807.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.657

Publications

10 publications found

Variant links:

Genes affected

CIDEB (HGNC:1977): (cell death inducing DFFA like effector b) Enables identical protein binding activity. Involved in activation of cysteine-type endopeptidase activity; positive regulation of cell death; and positive regulation of release of cytochrome c from mitochondria. Acts upstream of or within apoptotic process. Located in cytosol and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

CIDEB links:

LTB4R2 (HGNC:19260): (leukotriene B4 receptor 2) Predicted to enable G protein-coupled peptide receptor activity and leukotriene B4 receptor activity. Predicted to be involved in inflammatory response and neuropeptide signaling pathway. Predicted to act upstream of or within keratinocyte migration and signal transduction. Located in nucleoplasm and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

LTB4R2 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=-0.83).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein	UniProt
CIDEB	NM_001393334.1 link	c.-1021G>A	5_prime_UTR_variant	Exon 2 of 7	NP_001380263.1
CIDEB	NM_001318807.3 link	c.-414-607G>A	intron_variant	Intron 2 of 7	NP_001305736.1	Q9UHD4
CIDEB	NM_001393335.1 link	c.-447-607G>A	intron_variant	Intron 1 of 6	NP_001380264.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
CIDEB	ENST00000258807.5 link	c.-414-607G>A	intron_variant	Intron 1 of 6	1	ENSP00000258807.5	Q9UHD4
LTB4R2	ENST00000528054.1 link	c.-1135C>T	5_prime_UTR_variant	Exon 1 of 1	6	ENSP00000432146.1	A0A3Q5ACI7
CIDEB	ENST00000336557.9 link	c.-414-607G>A	intron_variant	Intron 2 of 7	2	ENSP00000337731.5	Q9UHD4
LTB4R2	ENST00000527924.6 link	c.-95-734C>T	intron_variant	Intron 1 of 2	3	ENSP00000436668.2	E9PIC1

Frequencies

GnomAD3 genomes

AF:

0.184

AC:

27967

AN:

152028

Hom.:

2931

Cov.:

show subpopulations

Gnomad AFR

AF:

0.158

Gnomad AMI

AF:

0.127

Gnomad AMR

AF:

0.287

Gnomad ASJ

AF:

0.188

Gnomad EAS

AF:

0.00193

Gnomad SAS

AF:

0.105

Gnomad FIN

AF:

0.132

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.205

Gnomad OTH

AF:

0.188

GnomAD4 exome

AF:

0.148

AC:

AN:

Hom.:

Cov.:

AF XY:

0.156

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

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:

0.300

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.139

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

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:

0.184

AC:

27980

AN:

152146

Hom.:

2932

Cov.:

AF XY:

0.179

AC XY:

13276

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.157

AC:

6530

AN:

41488

American (AMR)

AF:

0.287

AC:

4395

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.188

AC:

654

AN:

3470

East Asian (EAS)

AF:

0.00193

AC:

AN:

5178

South Asian (SAS)

AF:

0.105

AC:

508

AN:

4826

European-Finnish (FIN)

AF:

0.132

AC:

1392

AN:

10580

Middle Eastern (MID)

AF:

0.0816

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.205

AC:

13958

AN:

67996

Other (OTH)

AF:

0.186

AC:

393

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1174

2347

3521

4694

5868

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

290

580

870

1160

1450

<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:

0.193

Hom.:

487

Bravo

AF:

0.195

Asia WGS

AF:

0.0630

AC:

217

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

2.4

(source)

DANN

Benign

0.71

PhyloP100

-0.66

PromoterAI

-0.062

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.1

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

Computational scores

Splicing

Publications

Other links and lift over