chr18-69899351-C-T

Variant names:

• chr18-69899351-C-T
• rs1788234
• NM_001303618.2:c.383-3306G>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.383-3306G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 152,068 control chromosomes in the GnomAD database, including 17,123 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 0.46 (17123 hom., cov: 32)
• Consequence: CD226 NM_001303618.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.144
• Publications: 9 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.624 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.383-3306G>A		intron	N/A	NP_001290547.1
	CD226	NM_006566.4		c.383-3306G>A		intron	N/A	NP_006557.2
	CD226	NM_001303619.2		c.-83-3306G>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.383-3306G>A		intron	N/A	ENSP00000461947.1
	CD226	ENST00000280200.8	TSL:1	c.383-3306G>A		intron	N/A	ENSP00000280200.4
	CD226	ENST00000581982.5	TSL:1	c.-83-3306G>A		intron	N/A	ENSP00000464084.1

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69896 AN: 151950 Hom.: 17093 Cov.: 32

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.460 AC: 69985 AN: 152068 Hom.: 17123 Cov.: 32 AF XY: 0.454 AC XY: 33733 AN XY: 74336

African (AFR) AF: 0.630 AC: 26132 AN: 41472

American (AMR) AF: 0.402 AC: 6142 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1591 AN: 3472

East Asian (EAS) AF: 0.337 AC: 1743 AN: 5168

South Asian (SAS) AF: 0.452 AC: 2177 AN: 4816

European-Finnish (FIN) AF: 0.331 AC: 3499 AN: 10564

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27282 AN: 67988

Other (OTH) AF: 0.457 AC: 964 AN: 2110

Alfa AF: 0.423 Hom.: 26403

Bravo AF: 0.472

Asia WGS AF: 0.422 AC: 1467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.3
DANN	Benign	0.81
PhyloP100		0.14
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: rs1788234; hg19: chr18-67566587;