20-23079620-A-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_012072.4(CD93):c.*4330T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.877 in 152,226 control chromosomes in the GnomAD database, including 58,716 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 0.88 ( 58714 hom., cov: 33)
Exomes 𝑓: 1.0 ( 2 hom. )
Consequence
CD93
NM_012072.4 3_prime_UTR
NM_012072.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.18
Genes affected
CD93 (HGNC:15855): (CD93 molecule) The protein encoded by this gene is a cell-surface glycoprotein and type I membrane protein that was originally identified as a myeloid cell-specific marker. The encoded protein was once thought to be a receptor for C1q, but now is thought to instead be involved in intercellular adhesion and in the clearance of apoptotic cells. The intracellular cytoplasmic tail of this protein has been found to interact with moesin, a protein known to play a role in linking transmembrane proteins to the cytoskeleton and in the remodelling of the cytoskeleton. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CD93 | NM_012072.4 | c.*4330T>C | 3_prime_UTR_variant | 2/2 | ENST00000246006.5 | NP_036204.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CD93 | ENST00000246006.5 | c.*4330T>C | 3_prime_UTR_variant | 2/2 | 1 | NM_012072.4 | ENSP00000246006.4 |
Frequencies
GnomAD3 genomes AF: 0.877 AC: 133366AN: 152102Hom.: 58684 Cov.: 33
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GnomAD4 exome AF: 1.00 AC: 4AN: 4Hom.: 2 Cov.: 0 AF XY: 1.00 AC XY: 2AN XY: 2
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GnomAD4 genome AF: 0.877 AC: 133452AN: 152222Hom.: 58714 Cov.: 33 AF XY: 0.874 AC XY: 65056AN XY: 74430
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at