dbSNP rs16840096: CD1B:c.*66G>A (chr1-158328170-C-T) – 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.*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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.624

Publications

3 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=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD1B	NM_001764.3 link	c.*66G>A		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.*66G>A		3_prime_UTR_variant	Exon 6 of 6	1	NM_001764.3	ENSP00000357150.3		P29016-1
CD1B	ENST00000451207.5 link	c.*66G>A		3_prime_UTR_variant	Exon 5 of 5	3		ENSP00000395161.1		H7C0I2

Frequencies

GnomAD3 genomes

AF:

0.120

AC:

18239

AN:

151948

Hom.:

1438

Cov.:

show subpopulations

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.:

AF XY:

0.141

AC XY:

75671

AN XY:

536412

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

5827

11654

17481

23308

29135

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2912

5824

8736

11648

14560

<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:

0.120

AC:

18241

AN:

152066

Hom.:

1437

Cov.:

AF XY:

0.124

AC XY:

9205

AN XY:

74312

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.126

AC:

8580

AN:

67982

Other (OTH)

AF:

0.119

AC:

251

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

785

1570

2355

3140

3925

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

216

432

648

864

1080

<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:

0.122

Hom.:

1550

Bravo

AF:

0.116

Asia WGS

AF:

0.274

AC:

953

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.9

(source)

DANN

Benign

0.40

PhyloP100

-0.62

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