rs3176842

Variant names:

• chr1-158328567-G-A
• rs3176842
• NM_001764.3:c.981-310C>T

Variant summary

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

The NM_001764.3(CD1B):​c.981-310C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 152,024 control chromosomes in the GnomAD database, including 14,381 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 0.38 (14381 hom., cov: 32)
• Consequence: CD1B NM_001764.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.520
• Publications: 2 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD1B	NM_001764.3	c.981-310C>T		intron_variant	Intron 5 of 5	ENST00000368168.4	NP_001755.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD1B	ENST00000368168.4	c.981-310C>T		intron_variant	Intron 5 of 5	1	NM_001764.3	ENSP00000357150.3
CD1B	ENST00000451207.5	c.717-310C>T		intron_variant	Intron 4 of 4	3		ENSP00000395161.1

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58035 AN: 151906 Hom.: 14342 Cov.: 32

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.382 AC: 58136 AN: 152024 Hom.: 14381 Cov.: 32 AF XY: 0.381 AC XY: 28345 AN XY: 74310

African (AFR) AF: 0.715 AC: 29633 AN: 41454

American (AMR) AF: 0.295 AC: 4509 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 964 AN: 3468

East Asian (EAS) AF: 0.281 AC: 1454 AN: 5174

South Asian (SAS) AF: 0.323 AC: 1557 AN: 4818

European-Finnish (FIN) AF: 0.288 AC: 3042 AN: 10556

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

European-Non Finnish (NFE) AF: 0.234 AC: 15905 AN: 67966

Other (OTH) AF: 0.332 AC: 702 AN: 2112

Alfa AF: 0.332 Hom.: 1276

Bravo AF: 0.393

Asia WGS AF: 0.350 AC: 1218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.0
DANN	Benign	0.38
PhyloP100		0.52
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: rs3176842; hg19: chr1-158298357;