dbSNP rs11583390: CD1B:c.*162G>T (chr1-158328074-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001764.3(CD1B):c.*162G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.042 in 607,354 control chromosomes in the GnomAD database, including 645 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 0.036 ( 130 hom., cov: 32)

Exomes 𝑓: 0.044 ( 515 hom. )

Consequence

CD1B
NM_001764.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.404

Publications

2 publications found

Variant links:

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]

CD1B links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD1B	NM_001764.3 link	c.*162G>T		3_prime_UTR_variant	Exon 6 of 6	ENST00000368168.4	NP_001755.1	P29016-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD1B	ENST00000368168.4 link	c.*162G>T		3_prime_UTR_variant	Exon 6 of 6	1	NM_001764.3	ENSP00000357150.3		P29016-1
CD1B	ENST00000451207.5 link	c.*162G>T		3_prime_UTR_variant	Exon 5 of 5	3		ENSP00000395161.1		H7C0I2

Frequencies

GnomAD3 genomes

AF:

0.0356

AC:

5417

AN:

152022

Hom.:

130

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00846

Gnomad AMI

AF:

0.0219

Gnomad AMR

AF:

0.0303

Gnomad ASJ

AF:

0.0346

Gnomad EAS

AF:

0.0444

Gnomad SAS

AF:

0.0361

Gnomad FIN

AF:

0.0763

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0465

Gnomad OTH

AF:

0.0427

GnomAD4 exome

AF:

0.0442

AC:

20109

AN:

455214

Hom.:

515

Cov.:

AF XY:

0.0434

AC XY:

10469

AN XY:

240956

show subpopulations

African (AFR)

AF:

0.00919

AC:

115

AN:

12508

American (AMR)

AF:

0.0231

AC:

413

AN:

17910

Ashkenazi Jewish (ASJ)

AF:

0.0311

AC:

414

AN:

13322

East Asian (EAS)

AF:

0.0537

AC:

1622

AN:

30220

South Asian (SAS)

AF:

0.0369

AC:

1415

AN:

38340

European-Finnish (FIN)

AF:

0.0792

AC:

2936

AN:

37060

Middle Eastern (MID)

AF:

0.0295

AC:

AN:

2782

European-Non Finnish (NFE)

AF:

0.0436

AC:

12100

AN:

277494

Other (OTH)

AF:

0.0396

AC:

1012

AN:

25578

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

875

1750

2624

3499

4374

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

114

228

342

456

570

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0356

AC:

5417

AN:

152140

Hom.:

130

Cov.:

AF XY:

0.0363

AC XY:

2700

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.00850

AC:

353

AN:

41512

American (AMR)

AF:

0.0302

AC:

462

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.0346

AC:

120

AN:

3468

East Asian (EAS)

AF:

0.0441

AC:

229

AN:

5190

South Asian (SAS)

AF:

0.0363

AC:

175

AN:

4818

European-Finnish (FIN)

AF:

0.0763

AC:

807

AN:

10576

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0465

AC:

3159

AN:

67980

Other (OTH)

AF:

0.0422

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

268

537

805

1074

1342

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

136

204

272

340

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0421

Hom.:

311

Bravo

AF:

0.0314

Asia WGS

AF:

0.0300

AC:

104

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.7

(source)

DANN

Benign

0.55

PhyloP100

-0.40

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over