Variant rs1800051 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001775.4(CD38):c.504A>C(p.Ile168Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.046 in 1,596,590 control chromosomes in the GnomAD database, including 2,505 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 0.059 ( 357 hom., cov: 32)

Exomes 𝑓: 0.045 ( 2148 hom. )

Consequence

CD38
NM_001775.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0100

Variant links:

Genes affected

CD38 (HGNC:1667): (CD38 molecule) The protein encoded by this gene is a non-lineage-restricted, type II transmembrane glycoprotein that synthesizes and hydrolyzes cyclic adenosine 5'-diphosphate-ribose, an intracellular calcium ion mobilizing messenger. The release of soluble protein and the ability of membrane-bound protein to become internalized indicate both extracellular and intracellular functions for the protein. This protein has an N-terminal cytoplasmic tail, a single membrane-spanning domain, and a C-terminal extracellular region with four N-glycosylation sites. Crystal structure analysis demonstrates that the functional molecule is a dimer, with the central portion containing the catalytic site. It is used as a prognostic marker for patients with chronic lymphocytic leukemia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2015]

CD38 links:

CD38 (HGNC:):

CD38 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BP7

Synonymous conserved (PhyloP=0.01 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD38	NM_001775.4 linkuse as main transcript	c.504A>C	p.Ile168Ile	synonymous_variant	4/8	ENST00000226279.8	NP_001766.2	P28907-1B4E006
CD38	NR_132660.2 linkuse as main transcript	n.455A>C		non_coding_transcript_exon_variant	3/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
CD38	ENST00000226279.8 linkuse as main transcript	c.504A>C	p.Ile168Ile	synonymous_variant	4/8	1	NM_001775.4	ENSP00000226279.2	P28907-1
CD38	ENST00000502843.5 linkuse as main transcript	n.368A>C		non_coding_transcript_exon_variant	3/7	1		ENSP00000427277.1	P28907-2
CD38	ENST00000510674.1 linkuse as main transcript	c.168A>C	p.Ile56Ile	synonymous_variant	3/6	5		ENSP00000423047.1	H0Y950

Frequencies

GnomAD3 genomes

AF:

0.0585

AC:

8896

AN:

152136

Hom.:

355

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0868

Gnomad AMI

AF:

0.00658

Gnomad AMR

AF:

0.0548

Gnomad ASJ

AF:

0.0369

Gnomad EAS

AF:

0.176

Gnomad SAS

AF:

0.0818

Gnomad FIN

AF:

0.0319

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0369

Gnomad OTH

AF:

0.0731

GnomAD3 exomes

AF:

0.0620

AC:

15576

AN:

251324

Hom.:

779

AF XY:

0.0594

AC XY:

8067

AN XY:

135834

show subpopulations

Gnomad AFR exome

AF:

0.0865

Gnomad AMR exome

AF:

0.0889

Gnomad ASJ exome

AF:

0.0425

Gnomad EAS exome

AF:

0.190

Gnomad SAS exome

AF:

0.0689

Gnomad FIN exome

AF:

0.0304

Gnomad NFE exome

AF:

0.0358

Gnomad OTH exome

AF:

0.0551

GnomAD4 exome

AF:

0.0447

AC:

64492

AN:

1444336

Hom.:

2148

Cov.:

AF XY:

0.0451

AC XY:

32476

AN XY:

719832

show subpopulations

Gnomad4 AFR exome

AF:

0.0892

Gnomad4 AMR exome

AF:

0.0843

Gnomad4 ASJ exome

AF:

0.0412

Gnomad4 EAS exome

AF:

0.160

Gnomad4 SAS exome

AF:

0.0691

Gnomad4 FIN exome

AF:

0.0304

Gnomad4 NFE exome

AF:

0.0356

Gnomad4 OTH exome

AF:

0.0569

GnomAD4 genome

AF:

0.0585

AC:

8907

AN:

152254

Hom.:

357

Cov.:

AF XY:

0.0583

AC XY:

4341

AN XY:

74460

show subpopulations

Gnomad4 AFR

AF:

0.0868

Gnomad4 AMR

AF:

0.0549

Gnomad4 ASJ

AF:

0.0369

Gnomad4 EAS

AF:

0.176

Gnomad4 SAS

AF:

0.0814

Gnomad4 FIN

AF:

0.0319

Gnomad4 NFE

AF:

0.0369

Gnomad4 OTH

AF:

0.0728

Alfa

AF:

0.0428

Hom.:

354

Bravo

AF:

0.0629

Asia WGS

AF:

0.141

AC:

490

AN:

3478

EpiCase

AF:

0.0405

EpiControl

AF:

0.0375

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

5.6

DANN

Benign

0.61

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over