Genetic Variant CIDEB:c.-414-638G>T (chr14-24309468-C-A) – 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.-414-638G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,280 control chromosomes in the GnomAD database, including 2,367 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 0.15 ( 2366 hom., cov: 32)

Exomes 𝑓: 0.082 ( 1 hom. )

Consequence

CIDEB
ENST00000258807.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.422

Publications

11 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=-0.79).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
CIDEB	NM_001393334.1 link	c.-1052G>T	5_prime_UTR_variant	Exon 2 of 7	NP_001380263.1
CIDEB	NM_001318807.3 link	c.-414-638G>T	intron_variant	Intron 2 of 7	NP_001305736.1
CIDEB	NM_001393335.1 link	c.-447-638G>T	intron_variant	Intron 1 of 6	NP_001380264.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein
CIDEB	ENST00000258807.5 link	c.-414-638G>T	intron_variant	Intron 1 of 6	1	ENSP00000258807.5
LTB4R2	ENST00000528054.1 link	c.-1104C>A	5_prime_UTR_variant	Exon 1 of 1	6	ENSP00000432146.1
CIDEB	ENST00000336557.9 link	c.-414-638G>T	intron_variant	Intron 2 of 7	2	ENSP00000337731.5
LTB4R2	ENST00000527924.6 link	c.-95-703C>A	intron_variant	Intron 1 of 2	3	ENSP00000436668.2

Frequencies

GnomAD3 genomes

AF:

0.150

AC:

22852

AN:

152052

Hom.:

2365

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0413

Gnomad AMI

AF:

0.127

Gnomad AMR

AF:

0.274

Gnomad ASJ

AF:

0.188

Gnomad EAS

AF:

0.00193

Gnomad SAS

AF:

0.105

Gnomad FIN

AF:

0.132

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.205

Gnomad OTH

AF:

0.164

GnomAD4 exome

AF:

0.0818

AC:

AN:

110

Hom.:

Cov.:

AF XY:

0.0972

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)

AF:

0.00

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:

0.0625

AC:

AN:

Other (OTH)

AF:

0.125

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.596

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:

0.150

AC:

22857

AN:

152170

Hom.:

2366

Cov.:

AF XY:

0.147

AC XY:

10914

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.0412

AC:

1710

AN:

41528

American (AMR)

AF:

0.274

AC:

4186

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.188

AC:

653

AN:

3470

East Asian (EAS)

AF:

0.00193

AC:

AN:

5182

South Asian (SAS)

AF:

0.106

AC:

509

AN:

4822

European-Finnish (FIN)

AF:

0.132

AC:

1397

AN:

10586

Middle Eastern (MID)

AF:

0.0748

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.205

AC:

13913

AN:

67990

Other (OTH)

AF:

0.162

AC:

341

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

958

1916

2874

3832

4790

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

244

488

732

976

1220

<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:

0.182

Hom.:

584

Bravo

AF:

0.156

Asia WGS

AF:

0.0560

AC:

193

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

8.2

(source)

DANN

Benign

0.82

PhyloP100

0.42

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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