NM_001371762.2:c.887-200T>C

Variant names:

• chr1-158183736-T-C
• rs692565
• NM_001371762.2:c.887-200T>C

Variant summary

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

The NM_001371762.2(CD1D):​c.887-200T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 152,038 control chromosomes in the GnomAD database, including 20,557 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 (20557 hom., cov: 33)
• Consequence: CD1D NM_001371762.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214
• Publications: 10 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD1D	NM_001371762.2	c.887-200T>C		intron_variant	Intron 4 of 5	ENST00000674085.2	NP_001358691.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD1D	ENST00000674085.2	c.887-200T>C		intron_variant	Intron 4 of 5		NM_001371762.2	ENSP00000501100.1

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77663 AN: 151916 Hom.: 20542 Cov.: 33

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.511 AC: 77722 AN: 152038 Hom.: 20557 Cov.: 33 AF XY: 0.511 AC XY: 37968 AN XY: 74280

African (AFR) AF: 0.392 AC: 16261 AN: 41486

American (AMR) AF: 0.540 AC: 8239 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1762 AN: 3468

East Asian (EAS) AF: 0.758 AC: 3912 AN: 5164

South Asian (SAS) AF: 0.583 AC: 2806 AN: 4812

European-Finnish (FIN) AF: 0.511 AC: 5389 AN: 10556

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

European-Non Finnish (NFE) AF: 0.555 AC: 37723 AN: 67968

Other (OTH) AF: 0.499 AC: 1053 AN: 2110

Alfa AF: 0.540 Hom.: 65841

Bravo AF: 0.507

Asia WGS AF: 0.587 AC: 2043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.5
DANN	Benign	0.47
PhyloP100		-0.21
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs692565; hg19: chr1-158153526;