rs11583390

Positions:

• chr1-158328074-C-A

Variant summary

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

The NM_001764.3(CD1B):​c.*162G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.042 in 607,354 control chromosomes in the GnomAD database, including 645 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 0.036 (130 hom., cov: 32)
  • Exomes 𝑓: 0.044 (515 hom.)
• Consequence: CD1B NM_001764.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.404

Genes affected

CD1B (HGNC:1635): (CD1b molecule) This gene encodes a member of the CD1 family of transmembrane glycoproteins, which are structurally related to the major histocompatibility complex (MHC) proteins and form heterodimers with beta-2-microglobulin. The CD1 proteins mediate the presentation of primarily lipid and glycolipid antigens of self or microbial origin to T cells. The human genome contains five CD1 family genes organized in a cluster on chromosome 1. The CD1 family members are thought to differ in their cellular localization and specificity for particular lipid ligands. The protein encoded by this gene localizes to late endosomes and lysosomes via a tyrosine-based motif in the cytoplasmic tail, and requires vesicular acidification to bind lipid antigens. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD1B	NM_001764.3	c.*162G>T		3_prime_UTR_variant	6/6	ENST00000368168.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD1B	ENST00000368168.4	c.*162G>T		3_prime_UTR_variant	6/6	1	NM_001764.3	P1
CD1B	ENST00000451207.5	c.*162G>T		3_prime_UTR_variant	5/5	3

Frequencies

GnomAD3 genomes AF: 0.0356 AC: 5417 AN: 152022 Hom.: 130 Cov.: 32

Gnomad AFR AF: 0.00846

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0303

Gnomad ASJ AF: 0.0346

Gnomad EAS AF: 0.0444

Gnomad SAS AF: 0.0361

Gnomad FIN AF: 0.0763

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0465

Gnomad OTH AF: 0.0427

GnomAD4 exome AF: 0.0442 AC: 20109 AN: 455214 Hom.: 515 Cov.: 6 AF XY: 0.0434 AC XY: 10469 AN XY: 240956

Gnomad4 AFR exome AF: 0.00919

Gnomad4 AMR exome AF: 0.0231

Gnomad4 ASJ exome AF: 0.0311

Gnomad4 EAS exome AF: 0.0537

Gnomad4 SAS exome AF: 0.0369

Gnomad4 FIN exome AF: 0.0792

Gnomad4 NFE exome AF: 0.0436

Gnomad4 OTH exome AF: 0.0396

GnomAD4 genome AF: 0.0356 AC: 5417 AN: 152140 Hom.: 130 Cov.: 32 AF XY: 0.0363 AC XY: 2700 AN XY: 74362

Gnomad4 AFR AF: 0.00850

Gnomad4 AMR AF: 0.0302

Gnomad4 ASJ AF: 0.0346

Gnomad4 EAS AF: 0.0441

Gnomad4 SAS AF: 0.0363

Gnomad4 FIN AF: 0.0763

Gnomad4 NFE AF: 0.0465

Gnomad4 OTH AF: 0.0422

Alfa AF: 0.0415 Hom.: 138

Bravo AF: 0.0314

Asia WGS AF: 0.0300 AC: 104 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.55

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs11583390; hg19: chr1-158297864;