chr18-69849610-A-C

Variant names:

• chr18-69849610-A-C
• rs893001
• ENST00000578928.1:n.110-7215T>G

Variant summary

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

The ENST00000578928.1(CD226):​n.110-7215T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.17 (195 hom., cov: 0)
• Consequence: CD226 ENST00000578928.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 13 publications found

Genes affected

CD226 (HGNC:16961): (CD226 molecule) This gene encodes a glycoprotein expressed on the surface of NK cells, platelets, monocytes and a subset of T cells. It is a member of the Ig-superfamily containing 2 Ig-like domains of the V-set. The protein mediates cellular adhesion of platelets and megakaryocytic cells to vascular endothelial cells. The protein also plays a role in megakaryocytic cell maturation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000578928.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD226	ENST00000578928.1	TSL:4	n.110-7215T>G		intron	N/A	ENSP00000463152.1

Frequencies

GnomAD3 genomes AF: 0.173 AC: 5242 AN: 30252 Hom.: 195 Cov.: 0

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.0935

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0900

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.174 AC: 5259 AN: 30288 Hom.: 195 Cov.: 0 AF XY: 0.173 AC XY: 2527 AN XY: 14612

African (AFR) AF: 0.235 AC: 3346 AN: 14248

American (AMR) AF: 0.158 AC: 377 AN: 2388

Ashkenazi Jewish (ASJ) AF: 0.0935 AC: 49 AN: 524

East Asian (EAS) AF: 0.260 AC: 245 AN: 944

South Asian (SAS) AF: 0.128 AC: 131 AN: 1020

European-Finnish (FIN) AF: 0.106 AC: 114 AN: 1076

Middle Eastern (MID) AF: 0.122 AC: 10 AN: 82

European-Non Finnish (NFE) AF: 0.0900 AC: 831 AN: 9238

Other (OTH) AF: 0.149 AC: 63 AN: 424

Alfa AF: 0.521 Hom.: 11259

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.82
DANN	Benign	0.47
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs893001; hg19: chr18-67516846; COSMIC: COSV66930141;