rs17208112

chr18-69890193-G-A

Variant summary

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

The NM_001303618.2(CD226):c.727+5508C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,154 control chromosomes in the GnomAD database, including 3,736 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 0.20 (3736 hom., cov: 32)
• Consequence: CD226 NM_001303618.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.901

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD226	NM_001303618.2	c.727+5508C>T		intron_variant		ENST00000582621.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD226	ENST00000582621.6	c.727+5508C>T		intron_variant		1	NM_001303618.2	P1

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30684 AN: 152036 Hom.: 3735 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.00558

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.202 AC: 30696 AN: 152154 Hom.: 3736 Cov.: 32 AF XY: 0.195 AC XY: 14521 AN XY: 74398

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.00559

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.247

Alfa AF: 0.269 Hom.: 7092

Bravo AF: 0.198

Asia WGS AF: 0.127 AC: 445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.50
Dann	Benign	0.73

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs17208112; hg19: chr18-67557429;