rs12604328

Variant names:

• chr18-69857737-T-C
• rs12604328
• NM_001303618.2:c.*6577A>G

Your query was ambiguous. Multiple possible variants found:

• chr18-69857737-T-C
• chr18-69857737-T-G

Variant summary

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

The NM_001303618.2(CD226):​c.*6577A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,120 control chromosomes in the GnomAD database, including 4,153 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 0.22 (4153 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: CD226 NM_001303618.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• 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 = 0.308 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.*6577A>G		3_prime_UTR	Exon 6 of 6	NP_001290547.1	Q15762
	CD226	NM_006566.4		c.*6577A>G		3_prime_UTR	Exon 7 of 7	NP_006557.2	Q15762
	CD226	NM_001303619.2		c.*6577A>G		3_prime_UTR	Exon 5 of 5	NP_001290548.1	J3QR77

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD226	ENST00000582621.6	TSL:1 MANE Select	c.*6577A>G		3_prime_UTR	Exon 6 of 6	ENSP00000461947.1	Q15762
	CD226	ENST00000280200.8	TSL:1	c.*6577A>G		3_prime_UTR	Exon 7 of 7	ENSP00000280200.4	Q15762
	CD226	ENST00000578928.1	TSL:4	n.110-15342A>G		intron	N/A	ENSP00000463152.1	J3QKM7

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34134 AN: 152002 Hom.: 4152 Cov.: 33

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.253

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

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) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.224 AC: 34144 AN: 152120 Hom.: 4153 Cov.: 33 AF XY: 0.225 AC XY: 16744 AN XY: 74350

African (AFR) AF: 0.134 AC: 5574 AN: 41510

American (AMR) AF: 0.271 AC: 4135 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 868 AN: 3472

East Asian (EAS) AF: 0.231 AC: 1197 AN: 5180

South Asian (SAS) AF: 0.321 AC: 1547 AN: 4822

European-Finnish (FIN) AF: 0.198 AC: 2089 AN: 10574

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.263 AC: 17893 AN: 67976

Other (OTH) AF: 0.250 AC: 529 AN: 2112

Alfa AF: 0.258 Hom.: 11282

Bravo AF: 0.227

Asia WGS AF: 0.241 AC: 837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.74
PhyloP100		-1.1

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: rs12604328; hg19: chr18-67524973;