rs1800051

Variant summary

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

The NM_001775.4(CD38):ā€‹c.504A>Cā€‹(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: š‘“ 0.059 ( 357 hom., cov: 32)
Exomes š‘“: 0.045 ( 2148 hom. )

Consequence

CD38
NM_001775.4 synonymous

Scores

2

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]

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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
CD38NM_001775.4 linkuse as main transcriptc.504A>C p.Ile168Ile synonymous_variant 4/8 ENST00000226279.8 NP_001766.2 P28907-1B4E006
CD38NR_132660.2 linkuse as main transcriptn.455A>C non_coding_transcript_exon_variant 3/7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CD38ENST00000226279.8 linkuse as main transcriptc.504A>C p.Ile168Ile synonymous_variant 4/81 NM_001775.4 ENSP00000226279.2 P28907-1
CD38ENST00000502843.5 linkuse as main transcriptn.368A>C non_coding_transcript_exon_variant 3/71 ENSP00000427277.1 P28907-2
CD38ENST00000510674.1 linkuse as main transcriptc.168A>C p.Ile56Ile synonymous_variant 3/65 ENSP00000423047.1 H0Y950

Frequencies

GnomAD3 genomes
AF:
0.0585
AC:
8896
AN:
152136
Hom.:
355
Cov.:
32
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.:
27
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.:
32
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.

Other links and lift over

dbSNP: rs1800051; hg19: chr4-15835844; COSMIC: COSV56890030; API