1-158180329-C-T

Variant names:

• chr1-158180329-C-T
• rs3754471
• ENST00000368171.5:c.-283-490C>T

Variant summary

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

The NM_001766.4(CD1D):​c.-284+167C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 151,910 control chromosomes in the GnomAD database, including 10,821 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 0.36 (10821 hom., cov: 31)
• Consequence: CD1D NM_001766.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD1D	NM_001371763.1	c.-283-490C>T		intron_variant	Intron 1 of 6		NP_001358692.1
CD1D	NM_001766.4	c.-284+167C>T		intron_variant	Intron 1 of 6		NP_001757.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD1D	ENST00000368171.5	c.-283-490C>T		intron_variant	Intron 1 of 6	1		ENSP00000357153.3
CD1D	ENST00000673723.4	c.-284+167C>T		intron_variant	Intron 1 of 6			ENSP00000501245.3

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55122 AN: 151792 Hom.: 10821 Cov.: 31

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.363 AC: 55132 AN: 151910 Hom.: 10821 Cov.: 31 AF XY: 0.358 AC XY: 26544 AN XY: 74226

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.376

Alfa AF: 0.422 Hom.: 17421

Bravo AF: 0.363

Asia WGS AF: 0.258 AC: 898 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	3.5
DANN	Benign	0.61

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.20		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.20		Position offset: -6

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

Publications

LitVar

Other links and lift over

dbSNP: rs3754471; hg19: chr1-158150119;