rs1065457

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

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

The NM_030893.4(CD1E):c.317A>G(p.Gln106Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 1,613,352 control chromosomes in the GnomAD database, including 143,697 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.51 ( 23277 hom., cov: 32)

Exomes 𝑓: 0.39 ( 120420 hom. )

Consequence

CD1E
NM_030893.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.94

Publications

42 publications found

Variant links:

Genes affected

CD1E (HGNC:1638): (CD1e 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 within Golgi compartments, endosomes, and lysosomes, and is cleaved into a stable soluble form. The soluble form is required for the intracellular processing of some glycolipids into a form that can be presented by other CD1 family members. Many alternatively spliced transcript variants encoding different isoforms have been described. Additional transcript variants have been found; however, their biological validity has not been determined. [provided by RefSeq, Jun 2010]

CD1E links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (MetaRNN=1.0941127E-6).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030893.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
CD1E	NM_030893.4	MANE Select	c.317A>G	p.Gln106Arg	missense	Exon 2 of 6	NP_112155.2
CD1E	NM_001042583.3		c.317A>G	p.Gln106Arg	missense	Exon 2 of 6	NP_001036048.1
CD1E	NM_001042585.3		c.317A>G	p.Gln106Arg	missense	Exon 2 of 6	NP_001036050.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
CD1E	ENST00000368167.8	TSL:1 MANE Select	c.317A>G	p.Gln106Arg	missense	Exon 2 of 6	ENSP00000357149.3
CD1E	ENST00000368160.7	TSL:1	c.317A>G	p.Gln106Arg	missense	Exon 2 of 6	ENSP00000357142.3
CD1E	ENST00000368163.7	TSL:1	c.317A>G	p.Gln106Arg	missense	Exon 2 of 6	ENSP00000357145.3

Frequencies

GnomAD3 genomes

AF:

0.515

AC:

78177

AN:

151934

Hom.:

23231

Cov.:

show subpopulations

Gnomad AFR

AF:

0.817

Gnomad AMI

AF:

0.419

Gnomad AMR

AF:

0.436

Gnomad ASJ

AF:

0.433

Gnomad EAS

AF:

0.661

Gnomad SAS

AF:

0.580

Gnomad FIN

AF:

0.400

Gnomad MID

AF:

0.465

Gnomad NFE

AF:

0.358

Gnomad OTH

AF:

0.456

GnomAD2 exomes

AF:

0.445

AC:

110587

AN:

248468

AF XY:

0.442

show subpopulations

Gnomad AFR exome

AF:

0.829

Gnomad AMR exome

AF:

0.414

Gnomad ASJ exome

AF:

0.422

Gnomad EAS exome

AF:

0.667

Gnomad FIN exome

AF:

0.396

Gnomad NFE exome

AF:

0.348

Gnomad OTH exome

AF:

0.419

GnomAD4 exome

AF:

0.394

AC:

575075

AN:

1461300

Hom.:

120420

Cov.:

AF XY:

0.397

AC XY:

288784

AN XY:

726958

show subpopulations

African (AFR)

AF:

0.836

AC:

27986

AN:

33466

American (AMR)

AF:

0.416

AC:

18578

AN:

44684

Ashkenazi Jewish (ASJ)

AF:

0.423

AC:

11041

AN:

26118

East Asian (EAS)

AF:

0.639

AC:

25377

AN:

39698

South Asian (SAS)

AF:

0.558

AC:

48159

AN:

86236

European-Finnish (FIN)

AF:

0.396

AC:

21153

AN:

53384

Middle Eastern (MID)

AF:

0.463

AC:

2666

AN:

5764

European-Non Finnish (NFE)

AF:

0.354

AC:

394033

AN:

1111580

Other (OTH)

AF:

0.432

AC:

26082

AN:

60370

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

17812

35624

53436

71248

89060

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

12986

25972

38958

51944

64930

<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:

0.515

AC:

78286

AN:

152052

Hom.:

23277

Cov.:

AF XY:

0.517

AC XY:

38437

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.817

AC:

33903

AN:

41490

American (AMR)

AF:

0.435

AC:

6651

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.433

AC:

1502

AN:

3470

East Asian (EAS)

AF:

0.661

AC:

3409

AN:

5160

South Asian (SAS)

AF:

0.580

AC:

2796

AN:

4818

European-Finnish (FIN)

AF:

0.400

AC:

4222

AN:

10556

Middle Eastern (MID)

AF:

0.480

AC:

141

AN:

294

European-Non Finnish (NFE)

AF:

0.358

AC:

24314

AN:

67968

Other (OTH)

AF:

0.458

AC:

968

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1619

3237

4856

6474

8093

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

652

1304

1956

2608

3260

<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:

0.409

Hom.:

50515

Bravo

AF:

0.523

TwinsUK

AF:

0.357

AC:

1324

ALSPAC

AF:

0.347

AC:

1337

ESP6500AA

AF:

0.781

AC:

3006

ESP6500EA

AF:

0.344

AC:

2869

ExAC

AF:

0.449

AC:

54260

Asia WGS

AF:

0.626

AC:

2178

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.064

BayesDel_addAF

Benign

-0.91

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.0010

(source)

DANN

Benign

0.35

DEOGEN2

Benign

0.0056

Eigen

Benign

-1.9

Eigen_PC

Benign

-1.9

FATHMM_MKL

Benign

0.00062

LIST_S2

Benign

0.020

MetaRNN

Benign

0.0000011

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.37

PhyloP100

-3.9

PrimateAI

Benign

0.25

PROVEAN

Benign

0.97

REVEL

Benign

0.063

Sift

Benign

1.0

Sift4G

Benign

1.0

Polyphen

0.0

Vest4

0.0050

MPC

0.060

ClinPred

0.0016

GERP RS

-5.5

Varity_R

0.025

gMVP

0.12

Mutation Taster

=99/1

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over