14-24310388-T-G

Variant names:

• chr14-24310388-T-G
• rs1950505
• NM_019839.5:c.-11+133T>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001393334.1(CIDEB):​c.-1972A>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.95 in 616,996 control chromosomes in the GnomAD database, including 278,907 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 0.94 (67701 hom., cov: 30)
  • Exomes 𝑓: 0.95 (211206 hom.)
• Consequence: CIDEB NM_001393334.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.234

Genes affected

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]

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LTB4R2	NM_019839.5	c.-11+133T>G		intron_variant	Intron 1 of 1	ENST00000533293.2	NP_062813.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LTB4R2	ENST00000533293.2	c.-11+133T>G		intron_variant	Intron 1 of 1	1	NM_019839.5	ENSP00000433290.1

Frequencies

GnomAD3 genomes AF: 0.943 AC: 143360 AN: 152030 Hom.: 67663 Cov.: 30

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.932

Gnomad ASJ AF: 0.963

Gnomad EAS AF: 0.849

Gnomad SAS AF: 0.948

Gnomad FIN AF: 0.975

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.964

Gnomad OTH AF: 0.945

GnomAD4 exome AF: 0.953 AC: 442906 AN: 464848 Hom.: 211206 Cov.: 2 AF XY: 0.953 AC XY: 235457 AN XY: 247060

Gnomad4 AFR exome AF: 0.913

Gnomad4 AMR exome AF: 0.932

Gnomad4 ASJ exome AF: 0.957

Gnomad4 EAS exome AF: 0.852

Gnomad4 SAS exome AF: 0.954

Gnomad4 FIN exome AF: 0.973

Gnomad4 NFE exome AF: 0.965

Gnomad4 OTH exome AF: 0.953

GnomAD4 genome AF: 0.943 AC: 143455 AN: 152148 Hom.: 67701 Cov.: 30 AF XY: 0.942 AC XY: 70086 AN XY: 74374

Gnomad4 AFR AF: 0.913

Gnomad4 AMR AF: 0.932

Gnomad4 ASJ AF: 0.963

Gnomad4 EAS AF: 0.849

Gnomad4 SAS AF: 0.947

Gnomad4 FIN AF: 0.975

Gnomad4 NFE AF: 0.964

Gnomad4 OTH AF: 0.946

Alfa AF: 0.951 Hom.: 11245

Bravo AF: 0.938

Asia WGS AF: 0.912 AC: 3173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.87

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1950505; hg19: chr14-24779594;