rs2749812

chr20-23082290-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012072.4(CD93):c.*1660T>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 0.836 in 152,168 control chromosomes in the GnomAD database, including 53,369 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 0.84 (53355 hom., cov: 32)
  • Exomes 𝑓: 0.91 (14 hom.)
• Consequence: CD93 NM_012072.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD93	NM_012072.4	c.*1660T>C		3_prime_UTR_variant	2/2	ENST00000246006.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD93	ENST00000246006.5	c.*1660T>C		3_prime_UTR_variant	2/2	1	NM_012072.4	P1

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127108 AN: 152018 Hom.: 53323 Cov.: 32

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.887

Gnomad AMR AF: 0.880

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.868

GnomAD4 exome AF: 0.912 AC: 31 AN: 34 Hom.: 14 Cov.: 0 AF XY: 1.00 AC XY: 22 AN XY: 22

Gnomad4 AFR exome AF: 0.500

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.917

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.836 AC: 127195 AN: 152134 Hom.: 53355 Cov.: 32 AF XY: 0.834 AC XY: 61978 AN XY: 74358

Gnomad4 AFR AF: 0.808

Gnomad4 AMR AF: 0.880

Gnomad4 ASJ AF: 0.897

Gnomad4 EAS AF: 0.954

Gnomad4 SAS AF: 0.883

Gnomad4 FIN AF: 0.759

Gnomad4 NFE AF: 0.838

Gnomad4 OTH AF: 0.868

Alfa AF: 0.839 Hom.: 39639

Bravo AF: 0.846

Asia WGS AF: 0.913 AC: 3175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.21
Dann	Benign	0.43

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2749812; hg19: chr20-23062927;