rs1950505

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr14-24310388-T-G
• chr14-24310388-T-A
• chr14-24310388-T-C

Variant summary

Our verdict is Benign. The variant received -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. Variant has been reported in ClinVar as (no stars).

• 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
• Publications: 10 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001393334.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LTB4R2	NM_019839.5	MANE Select	c.-11+133T>G		intron	N/A	NP_062813.2	Q9NPC1
	CIDEB	NM_001393334.1		c.-1972A>C		5_prime_UTR	Exon 2 of 7	NP_001380263.1	Q9UHD4
	LTB4R2	NM_001164692.3		c.-67+133T>G		intron	N/A	NP_001158164.1	Q9NPC1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LTB4R2	ENST00000533293.2	TSL:1 MANE Select	c.-11+133T>G		intron	N/A	ENSP00000433290.1	Q9NPC1
	LTB4R2	ENST00000543919.1	TSL:1	c.-67+133T>G		intron	N/A	ENSP00000445772.1	Q9NPC1
	LTB4R2	ENST00000530080.1	TSL:1	c.-67+133T>G		intron	N/A	ENSP00000434760.1	E9PNJ6

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

African (AFR) AF: 0.913 AC: 11603 AN: 12702

American (AMR) AF: 0.932 AC: 18698 AN: 20052

Ashkenazi Jewish (ASJ) AF: 0.957 AC: 13942 AN: 14570

East Asian (EAS) AF: 0.852 AC: 26773 AN: 31430

South Asian (SAS) AF: 0.954 AC: 45740 AN: 47948

European-Finnish (FIN) AF: 0.973 AC: 29840 AN: 30662

Middle Eastern (MID) AF: 0.973 AC: 2041 AN: 2098

European-Non Finnish (NFE) AF: 0.965 AC: 268656 AN: 278510

Other (OTH) AF: 0.953 AC: 25613 AN: 26876

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

African (AFR) AF: 0.913 AC: 37874 AN: 41488

American (AMR) AF: 0.932 AC: 14250 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.963 AC: 3342 AN: 3472

East Asian (EAS) AF: 0.849 AC: 4366 AN: 5144

South Asian (SAS) AF: 0.947 AC: 4563 AN: 4818

European-Finnish (FIN) AF: 0.975 AC: 10343 AN: 10608

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.964 AC: 65545 AN: 68010

Other (OTH) AF: 0.946 AC: 1995 AN: 2108

Alfa AF: 0.957 Hom.: 29439

Bravo AF: 0.938

Asia WGS AF: 0.912 AC: 3173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.87
PhyloP100		0.23
PromoterAI		-0.085	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1950505; hg19: chr14-24779594;