1-158185303-G-T

Variant names:

• chr1-158185303-G-T
• rs422236
• NM_001371762.2:c.*1153G>T

Variant summary

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

The NM_001371762.2(CD1D):​c.*1153G>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 0.511 in 151,984 control chromosomes in the GnomAD database, including 20,486 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 0.51 (20486 hom., cov: 32)
• Consequence: CD1D NM_001371762.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272
• Publications: 5 publications found

Genes affected

CD1D (HGNC:1637): (CD1d molecule) This gene encodes a divergent 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. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2016]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD1D	NM_001371762.2	c.*1153G>T		3_prime_UTR_variant	Exon 6 of 6	ENST00000674085.2	NP_001358691.1
CD1D	NM_001766.4	c.*1153G>T		3_prime_UTR_variant	Exon 7 of 7		NP_001757.1
CD1D	NM_001319145.2	c.*1153G>T		3_prime_UTR_variant	Exon 5 of 5		NP_001306074.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD1D	ENST00000674085.2	c.*1153G>T		3_prime_UTR_variant	Exon 6 of 6		NM_001371762.2	ENSP00000501100.1

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77547 AN: 151864 Hom.: 20470 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.511 AC: 77607 AN: 151984 Hom.: 20486 Cov.: 32 AF XY: 0.510 AC XY: 37912 AN XY: 74298

African (AFR) AF: 0.392 AC: 16257 AN: 41458

American (AMR) AF: 0.539 AC: 8233 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1755 AN: 3466

East Asian (EAS) AF: 0.757 AC: 3914 AN: 5170

South Asian (SAS) AF: 0.568 AC: 2737 AN: 4818

European-Finnish (FIN) AF: 0.511 AC: 5396 AN: 10552

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.555 AC: 37687 AN: 67928

Other (OTH) AF: 0.498 AC: 1052 AN: 2112

Alfa AF: 0.508 Hom.: 9437

Bravo AF: 0.507

Asia WGS AF: 0.581 AC: 2023 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.5
DANN	Benign	0.81
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs422236; hg19: chr1-158155093;