chr20-23078618-T-C

Variant names:

• chr20-23078618-T-C
• rs2749817
• ENST00000850633.1:n.*368+4964A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000850633.1(CD93):​n.*368+4964A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 152,106 control chromosomes in the GnomAD database, including 26,112 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 0.57 (26112 hom., cov: 32)
• Consequence: CD93 ENST00000850633.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.732
• Publications: 8 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000850633.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD93	ENST00000850633.1		n.*368+4964A>G		intron	N/A	ENSP00000520912.1
	CD93	ENST00000850634.1		n.*122+5210A>G		intron	N/A	ENSP00000520913.1
	CD93	ENST00000850635.1		n.*122+5210A>G		intron	N/A	ENSP00000520914.1

Frequencies

GnomAD3 genomes AF: 0.566 AC: 86101 AN: 151988 Hom.: 26094 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.629

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.566 AC: 86159 AN: 152106 Hom.: 26112 Cov.: 32 AF XY: 0.562 AC XY: 41773 AN XY: 74376

African (AFR) AF: 0.348 AC: 14431 AN: 41472

American (AMR) AF: 0.671 AC: 10257 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.738 AC: 2558 AN: 3468

East Asian (EAS) AF: 0.673 AC: 3482 AN: 5174

South Asian (SAS) AF: 0.694 AC: 3348 AN: 4826

European-Finnish (FIN) AF: 0.466 AC: 4927 AN: 10572

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44866 AN: 67988

Other (OTH) AF: 0.632 AC: 1337 AN: 2114

Alfa AF: 0.640 Hom.: 24852

Bravo AF: 0.573

Asia WGS AF: 0.696 AC: 2423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.7
DANN	Benign	0.77
PhyloP100		0.73

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2749817; hg19: chr20-23059255;