rs1800051
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001775.4(CD38):āc.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
NM_001775.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0100
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 |
---|---|---|---|---|---|---|---|---|
CD38 | NM_001775.4 | c.504A>C | p.Ile168Ile | synonymous_variant | 4/8 | ENST00000226279.8 | NP_001766.2 | |
CD38 | NR_132660.2 | n.455A>C | non_coding_transcript_exon_variant | 3/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CD38 | ENST00000226279.8 | c.504A>C | p.Ile168Ile | synonymous_variant | 4/8 | 1 | NM_001775.4 | ENSP00000226279.2 | ||
CD38 | ENST00000502843.5 | n.368A>C | non_coding_transcript_exon_variant | 3/7 | 1 | ENSP00000427277.1 | ||||
CD38 | ENST00000510674.1 | c.168A>C | p.Ile56Ile | synonymous_variant | 3/6 | 5 | ENSP00000423047.1 |
Frequencies
GnomAD3 genomes AF: 0.0585 AC: 8896AN: 152136Hom.: 355 Cov.: 32
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GnomAD3 exomes AF: 0.0620 AC: 15576AN: 251324Hom.: 779 AF XY: 0.0594 AC XY: 8067AN XY: 135834
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GnomAD4 exome AF: 0.0447 AC: 64492AN: 1444336Hom.: 2148 Cov.: 27 AF XY: 0.0451 AC XY: 32476AN XY: 719832
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GnomAD4 genome AF: 0.0585 AC: 8907AN: 152254Hom.: 357 Cov.: 32 AF XY: 0.0583 AC XY: 4341AN XY: 74460
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Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at