NM_001303618.2:c.*6904C>A

Variant names:

• chr18-69857410-G-T
• rs4891781
• NM_001303618.2:c.*6904C>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.*6904C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 152,028 control chromosomes in the GnomAD database, including 10,666 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 0.37 (10666 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: CD226 NM_001303618.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 7 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.398 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD226	NM_001303618.2	MANE Select	c.*6904C>A		3_prime_UTR	Exon 6 of 6	NP_001290547.1
	CD226	NM_006566.4		c.*6904C>A		3_prime_UTR	Exon 7 of 7	NP_006557.2
	CD226	NM_001303619.2		c.*6904C>A		3_prime_UTR	Exon 5 of 5	NP_001290548.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD226	ENST00000582621.6	TSL:1 MANE Select	c.*6904C>A		3_prime_UTR	Exon 6 of 6	ENSP00000461947.1
	CD226	ENST00000280200.8	TSL:1	c.*6904C>A		3_prime_UTR	Exon 7 of 7	ENSP00000280200.4
	CD226	ENST00000578928.1	TSL:4	n.110-15015C>A		intron	N/A	ENSP00000463152.1

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56356 AN: 151906 Hom.: 10652 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.402

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.371 AC: 56411 AN: 152024 Hom.: 10666 Cov.: 32 AF XY: 0.366 AC XY: 27168 AN XY: 74290

African (AFR) AF: 0.351 AC: 14546 AN: 41468

American (AMR) AF: 0.349 AC: 5326 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1298 AN: 3466

East Asian (EAS) AF: 0.243 AC: 1253 AN: 5162

South Asian (SAS) AF: 0.409 AC: 1971 AN: 4822

European-Finnish (FIN) AF: 0.308 AC: 3256 AN: 10568

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27330 AN: 67962

Other (OTH) AF: 0.403 AC: 852 AN: 2112

Alfa AF: 0.384 Hom.: 8254

Bravo AF: 0.377

Asia WGS AF: 0.321 AC: 1121 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.69
DANN	Benign	0.64
PhyloP100		-0.097

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: rs4891781; hg19: chr18-67524646;