rs893001

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr18-69849610-A-C
• chr18-69849610-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD226	ENST00000578928.1	n.110-7215T>G		intron_variant	Intron 1 of 3	4		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

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.0935

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.0900

Gnomad4 OTH AF: 0.149

Alfa AF: 0.446 Hom.: 1958

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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