rs11087413

Variant names:

• chr20-23084173-C-T
• rs11087413
• NM_012072.4:c.1934+86G>A

Your query was ambiguous. Multiple possible variants found:

• chr20-23084173-C-T
• chr20-23084173-C-A
• chr20-23084173-C-G

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_012072.4(CD93):​c.1934+86G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 1,519,054 control chromosomes in the GnomAD database, including 244,047 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.52 (21503 hom., cov: 32)
  • Exomes 𝑓: 0.57 (222544 hom.)
• Consequence: CD93 NM_012072.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0590
• Publications: 3 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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 20-23084173-C-T is Benign according to our data. Variant chr20-23084173-C-T is described in ClinVar as Benign. ClinVar VariationId is 2688534.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012072.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD93	NM_012072.4	MANE Select	c.1934+86G>A		intron	N/A	NP_036204.2	Q9NPY3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD93	ENST00000246006.5	TSL:1 MANE Select	c.1934+86G>A		intron	N/A	ENSP00000246006.4	Q9NPY3
	CD93	ENST00000850633.1		n.1934+86G>A		intron	N/A	ENSP00000520912.1	Q9NPY3
	CD93	ENST00000850634.1		n.1934+86G>A		intron	N/A	ENSP00000520913.1	Q9NPY3

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78359 AN: 151920 Hom.: 21487 Cov.: 32

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.582

GnomAD4 exome AF: 0.565 AC: 773002 AN: 1367016 Hom.: 222544 Cov.: 22 AF XY: 0.569 AC XY: 386902 AN XY: 679714

African (AFR) AF: 0.356 AC: 11264 AN: 31668

American (AMR) AF: 0.657 AC: 28045 AN: 42718

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 15615 AN: 23292

East Asian (EAS) AF: 0.796 AC: 31197 AN: 39168

South Asian (SAS) AF: 0.656 AC: 52241 AN: 79680

European-Finnish (FIN) AF: 0.396 AC: 18902 AN: 47766

Middle Eastern (MID) AF: 0.691 AC: 3778 AN: 5464

European-Non Finnish (NFE) AF: 0.557 AC: 579084 AN: 1040384

Other (OTH) AF: 0.578 AC: 32876 AN: 56876

GnomAD4 genome AF: 0.516 AC: 78416 AN: 152038 Hom.: 21503 Cov.: 32 AF XY: 0.513 AC XY: 38134 AN XY: 74324

African (AFR) AF: 0.360 AC: 14919 AN: 41482

American (AMR) AF: 0.614 AC: 9380 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2340 AN: 3472

East Asian (EAS) AF: 0.786 AC: 4046 AN: 5150

South Asian (SAS) AF: 0.678 AC: 3270 AN: 4820

European-Finnish (FIN) AF: 0.377 AC: 3988 AN: 10576

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.564 AC: 38324 AN: 67956

Other (OTH) AF: 0.585 AC: 1232 AN: 2106

Alfa AF: 0.386 Hom.: 1038

Bravo AF: 0.530

Asia WGS AF: 0.704 AC: 2449 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.9
DANN	Benign	0.63
PhyloP100		0.059
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11087413; hg19: chr20-23064810;