ENST00000799105.1:n.244C>T

Variant names:

• chr20-23065387-G-A
• rs2424513
• ENST00000799105.1:n.244C>T

Variant summary

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

The ENST00000799105.1(CD93):​n.244C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,102 control chromosomes in the GnomAD database, including 978 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 0.10 (978 hom., cov: 33)
• Consequence: CD93 ENST00000799105.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• Publications: 4 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]

LOC124904964 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904964	XR_007067745.1	n.438C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD93	ENST00000799105.1	n.244C>T		non_coding_transcript_exon_variant	Exon 2 of 2
CD93	ENST00000850633.1	n.*801C>T		non_coding_transcript_exon_variant	Exon 5 of 5			ENSP00000520912.1
CD93	ENST00000850634.1	n.*265C>T		non_coding_transcript_exon_variant	Exon 3 of 3			ENSP00000520913.1

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15221 AN: 151984 Hom.: 978 Cov.: 33

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0682

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.0380

Gnomad SAS AF: 0.0850

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0658

Gnomad OTH AF: 0.0679

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

GnomAD4 genome AF: 0.100 AC: 15235 AN: 152102 Hom.: 978 Cov.: 33 AF XY: 0.101 AC XY: 7495 AN XY: 74362

African (AFR) AF: 0.183 AC: 7595 AN: 41482

American (AMR) AF: 0.0680 AC: 1039 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0660 AC: 229 AN: 3470

East Asian (EAS) AF: 0.0381 AC: 197 AN: 5174

South Asian (SAS) AF: 0.0847 AC: 408 AN: 4818

European-Finnish (FIN) AF: 0.106 AC: 1120 AN: 10572

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0658 AC: 4471 AN: 67990

Other (OTH) AF: 0.0672 AC: 142 AN: 2114

Alfa AF: 0.0892 Hom.: 87

Bravo AF: 0.0993

Asia WGS AF: 0.0520 AC: 181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.69
PhyloP100		0.0090

Splicing

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

Other links and lift over

dbSNP: rs2424513; hg19: chr20-23046024;