chr1-158328170-C-T

Variant names:

• chr1-158328170-C-T
• rs16840096
• NM_001764.3:c.*66G>A

Variant summary

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

The NM_001764.3(CD1B):​c.*66G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 1,197,052 control chromosomes in the GnomAD database, including 13,166 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 0.12 (1437 hom., cov: 32)
  • Exomes 𝑓: 0.14 (11729 hom.)
• Consequence: CD1B NM_001764.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.624
• Publications: 3 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

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.*66G>A		3_prime_UTR	Exon 6 of 6	NP_001755.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD1B	ENST00000368168.4	TSL:1 MANE Select	c.*66G>A		3_prime_UTR	Exon 6 of 6	ENSP00000357150.3
	CD1B	ENST00000451207.5	TSL:3	c.*66G>A		3_prime_UTR	Exon 5 of 5	ENSP00000395161.1

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18239 AN: 151948 Hom.: 1438 Cov.: 32

Gnomad AFR AF: 0.0541

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.120

GnomAD4 exome AF: 0.138 AC: 144133 AN: 1044986 Hom.: 11729 Cov.: 13 AF XY: 0.141 AC XY: 75671 AN XY: 536412

African (AFR) AF: 0.0529 AC: 1309 AN: 24762

American (AMR) AF: 0.136 AC: 5136 AN: 37790

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 3179 AN: 22566

East Asian (EAS) AF: 0.344 AC: 12903 AN: 37494

South Asian (SAS) AF: 0.234 AC: 16812 AN: 71738

European-Finnish (FIN) AF: 0.115 AC: 6038 AN: 52622

Middle Eastern (MID) AF: 0.172 AC: 836 AN: 4852

European-Non Finnish (NFE) AF: 0.122 AC: 91217 AN: 746904

Other (OTH) AF: 0.145 AC: 6703 AN: 46258

GnomAD4 genome AF: 0.120 AC: 18241 AN: 152066 Hom.: 1437 Cov.: 32 AF XY: 0.124 AC XY: 9205 AN XY: 74312

African (AFR) AF: 0.0539 AC: 2238 AN: 41504

American (AMR) AF: 0.139 AC: 2123 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 524 AN: 3466

East Asian (EAS) AF: 0.381 AC: 1970 AN: 5170

South Asian (SAS) AF: 0.256 AC: 1230 AN: 4812

European-Finnish (FIN) AF: 0.111 AC: 1170 AN: 10544

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8580 AN: 67982

Other (OTH) AF: 0.119 AC: 251 AN: 2110

Alfa AF: 0.122 Hom.: 1550

Bravo AF: 0.116

Asia WGS AF: 0.274 AC: 953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.40
PhyloP100		-0.62
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: rs16840096; hg19: chr1-158297960; COSMIC: COSV63804348;