20-23079620-A-G

Position:

• chr20-23079620-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.*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
• 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]

ACMG classification

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	UniProt
CD93	NM_012072.4	c.*4330T>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.*4330T>C		3_prime_UTR_variant	2/2	1	NM_012072.4	P1

Frequencies

GnomAD3 genomes AF: 0.877 AC: 133366 AN: 152102 Hom.: 58684 Cov.: 33

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.915

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.958

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.901

GnomAD4 exome AF: 1.00 AC: 4 AN: 4 Hom.: 2 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.877 AC: 133452 AN: 152222 Hom.: 58714 Cov.: 33 AF XY: 0.874 AC XY: 65056 AN XY: 74430

Gnomad4 AFR AF: 0.802

Gnomad4 AMR AF: 0.915

Gnomad4 ASJ AF: 0.910

Gnomad4 EAS AF: 0.958

Gnomad4 SAS AF: 0.888

Gnomad4 FIN AF: 0.846

Gnomad4 NFE AF: 0.908

Gnomad4 OTH AF: 0.901

Alfa AF: 0.907 Hom.: 55951

Bravo AF: 0.881

Asia WGS AF: 0.929 AC: 3231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.060
DANN	Benign	0.41

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: rs7492; hg19: chr20-23060257;