chr1-158325839-A-G

Position:

• chr1-158325839-A-G

Variant summary

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

The XM_017002784.3(CD1B):​c.607+4013T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 152,102 control chromosomes in the GnomAD database, including 21,782 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 0.50 (21782 hom., cov: 33)
• Consequence: CD1B XM_017002784.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD1B	XM_017002784.3	c.607+4013T>C		intron_variant			XP_016858273.1
CD1B	XM_017002785.3	c.607+4013T>C		intron_variant			XP_016858274.1
		n.158325839A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76390 AN: 151984 Hom.: 21744 Cov.: 33

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.452

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.503 AC: 76489 AN: 152102 Hom.: 21782 Cov.: 33 AF XY: 0.506 AC XY: 37586 AN XY: 74338

Gnomad4 AFR AF: 0.771

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.658

Gnomad4 SAS AF: 0.578

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.454

Alfa AF: 0.381 Hom.: 23535

Bravo AF: 0.509

Asia WGS AF: 0.624 AC: 2167 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10797007; hg19: chr1-158295629;