chr1-158328170-C-T

Position:

• chr1-158328170-C-T

Variant summary

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

The NM_001764.3(CD1B):​c.*66G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 1,197,052 control chromosomes in the GnomAD database, including 13,166 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 0.12 (1437 hom., cov: 32)
  • Exomes 𝑓: 0.14 (11729 hom.)
• Consequence: CD1B NM_001764.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.624

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD1B	NM_001764.3	c.*66G>A		3_prime_UTR_variant	6/6	ENST00000368168.4	NP_001755.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD1B	ENST00000368168.4	c.*66G>A		3_prime_UTR_variant	6/6	1	NM_001764.3	ENSP00000357150.3
CD1B	ENST00000451207.5	c.*66G>A		3_prime_UTR_variant	5/5	3		ENSP00000395161.1

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18239 AN: 151948 Hom.: 1438 Cov.: 32

Gnomad AFR AF: 0.0541

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.120

GnomAD4 exome AF: 0.138 AC: 144133 AN: 1044986 Hom.: 11729 Cov.: 13 AF XY: 0.141 AC XY: 75671 AN XY: 536412

Gnomad4 AFR exome AF: 0.0529

Gnomad4 AMR exome AF: 0.136

Gnomad4 ASJ exome AF: 0.141

Gnomad4 EAS exome AF: 0.344

Gnomad4 SAS exome AF: 0.234

Gnomad4 FIN exome AF: 0.115

Gnomad4 NFE exome AF: 0.122

Gnomad4 OTH exome AF: 0.145

GnomAD4 genome AF: 0.120 AC: 18241 AN: 152066 Hom.: 1437 Cov.: 32 AF XY: 0.124 AC XY: 9205 AN XY: 74312

Gnomad4 AFR AF: 0.0539

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.119

Alfa AF: 0.125 Hom.: 1226

Bravo AF: 0.116

Asia WGS AF: 0.274 AC: 953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.40

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: rs16840096; hg19: chr1-158297960; COSMIC: COSV63804348;