1-158312109-A-T

Variant names:

• chr1-158312109-A-T
• rs1590230
• XM_017002784.3:c.608-17071T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_017002784.3(CD1B):​c.608-17071T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 151,972 control chromosomes in the GnomAD database, including 8,203 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 0.32 (8203 hom., cov: 32)
• Consequence: CD1B XM_017002784.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD1B	XM_017002784.3	c.608-17071T>A		intron_variant	Intron 3 of 3		XP_016858273.1
CD1B	XM_017002785.3	c.607+17743T>A		intron_variant	Intron 3 of 3		XP_016858274.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48224 AN: 151854 Hom.: 8186 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.318 AC: 48287 AN: 151972 Hom.: 8203 Cov.: 32 AF XY: 0.322 AC XY: 23917 AN XY: 74262

African (AFR) AF: 0.427 AC: 17706 AN: 41434

American (AMR) AF: 0.368 AC: 5616 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 989 AN: 3472

East Asian (EAS) AF: 0.366 AC: 1893 AN: 5166

South Asian (SAS) AF: 0.322 AC: 1555 AN: 4826

European-Finnish (FIN) AF: 0.296 AC: 3125 AN: 10540

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16374 AN: 67962

Other (OTH) AF: 0.313 AC: 659 AN: 2108

Alfa AF: 0.160 Hom.: 293

Bravo AF: 0.325

Asia WGS AF: 0.385 AC: 1336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.1
DANN	Benign	0.60
PhyloP100		0.085

Splicing

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

Other links and lift over

dbSNP: rs1590230; hg19: chr1-158281899;