18-69898227-C-T

Variant names:

• chr18-69898227-C-T
• rs17208329
• NM_001303618.2:c.383-2182G>A

Variant summary

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

The NM_001303618.2(CD226):​c.383-2182G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 151,992 control chromosomes in the GnomAD database, including 3,171 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 (3171 hom., cov: 32)
• Consequence: CD226 NM_001303618.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.844
• Publications: 6 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]

ENSG00000304227 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001303618.2. 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
	CD226	NM_001303618.2	MANE Select	c.383-2182G>A		intron	N/A	NP_001290547.1
	CD226	NM_006566.4		c.383-2182G>A		intron	N/A	NP_006557.2
	CD226	NM_001303619.2		c.-83-2182G>A		intron	N/A	NP_001290548.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD226	ENST00000582621.6	TSL:1 MANE Select	c.383-2182G>A		intron	N/A	ENSP00000461947.1
	CD226	ENST00000280200.8	TSL:1	c.383-2182G>A		intron	N/A	ENSP00000280200.4
	CD226	ENST00000581982.5	TSL:1	c.-83-2182G>A		intron	N/A	ENSP00000464084.1

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29840 AN: 151874 Hom.: 3167 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.196 AC: 29846 AN: 151992 Hom.: 3171 Cov.: 32 AF XY: 0.196 AC XY: 14546 AN XY: 74278

African (AFR) AF: 0.127 AC: 5288 AN: 41478

American (AMR) AF: 0.176 AC: 2681 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 690 AN: 3470

East Asian (EAS) AF: 0.214 AC: 1102 AN: 5156

South Asian (SAS) AF: 0.223 AC: 1074 AN: 4814

European-Finnish (FIN) AF: 0.221 AC: 2322 AN: 10530

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15893 AN: 67958

Other (OTH) AF: 0.217 AC: 458 AN: 2106

Alfa AF: 0.214 Hom.: 7143

Bravo AF: 0.191

Asia WGS AF: 0.217 AC: 756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.55
DANN	Benign	0.59
PhyloP100		-0.84
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: rs17208329; hg19: chr18-67565463;