20-23084738-GTCC-G
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PM4_SupportingBP6
The NM_012072.4(CD93):c.1452_1454delGGA(p.Glu484del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000334 in 1,607,004 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.00034 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00033 ( 0 hom. )
Consequence
CD93
NM_012072.4 disruptive_inframe_deletion
NM_012072.4 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.249
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 Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_012072.4. Strenght limited to Supporting due to length of the change: 1aa.
BP6
Variant 20-23084738-GTCC-G is Benign according to our data. Variant chr20-23084738-GTCC-G is described in ClinVar as [Likely_benign]. Clinvar id is 3044385.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000342 AC: 52AN: 152128Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000588 AC: 143AN: 243236Hom.: 0 AF XY: 0.000651 AC XY: 86AN XY: 132076
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GnomAD4 exome AF: 0.000333 AC: 484AN: 1454758Hom.: 0 AF XY: 0.000352 AC XY: 255AN XY: 723632
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GnomAD4 genome AF: 0.000342 AC: 52AN: 152246Hom.: 0 Cov.: 33 AF XY: 0.000228 AC XY: 17AN XY: 74436
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
CD93-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 27, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at