1-158330516-G-A

Variant names:

• chr1-158330516-G-A
• rs962879
• NM_001764.3:c.328+280C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001764.3(CD1B):​c.328+280C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000213 in 468,670 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: CD1B NM_001764.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001764.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD1B	NM_001764.3	MANE Select	c.328+280C>T		intron	N/A	NP_001755.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD1B	ENST00000368168.4	TSL:1 MANE Select	c.328+280C>T		intron	N/A	ENSP00000357150.3
	CD1B	ENST00000451207.5	TSL:3	c.229+280C>T		intron	N/A	ENSP00000395161.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000213 AC: 1 AN: 468670 Hom.: 0 Cov.: 2 AF XY: 0.00000394 AC XY: 1 AN XY: 253852

African (AFR) AF: 0.00 AC: 0 AN: 13816

American (AMR) AF: 0.00 AC: 0 AN: 28998

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16090

East Asian (EAS) AF: 0.0000371 AC: 1 AN: 26934

South Asian (SAS) AF: 0.00 AC: 0 AN: 54734

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 26266

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3630

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 271964

Other (OTH) AF: 0.00 AC: 0 AN: 26238

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 138

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.33
DANN	Benign	0.69
PhyloP100		-2.3

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: rs962879; hg19: chr1-158300306;