18-69895747-GC-AT

Variant names:

• chr18-69895747-GC-AT
• NM_001303618.2:c.680_681delGCinsAT
• CD226 p.Ser227Asn

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001303618.2(CD226):​c.680_681delGCinsAT​(p.Ser227Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S227I) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CD226 NM_001303618.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560
• Publications: 0 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: Uncertain_significance. The variant received 0 ACMG points.

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.680_681delGCinsAT	p.Ser227Asn	missense	N/A	NP_001290547.1	Q15762
	CD226	NM_006566.4		c.680_681delGCinsAT	p.Ser227Asn	missense	N/A	NP_006557.2	Q15762
	CD226	NM_001303619.2		c.215_216delGCinsAT	p.Ser72Asn	missense	N/A	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.680_681delGCinsAT	p.Ser227Asn	missense	N/A	ENSP00000461947.1	Q15762
	CD226	ENST00000280200.8	TSL:1	c.680_681delGCinsAT	p.Ser227Asn	missense	N/A	ENSP00000280200.4	Q15762
	CD226	ENST00000581982.5	TSL:1	c.215_216delGCinsAT	p.Ser72Asn	missense	N/A	ENSP00000464084.1	J3QR77

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.056

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr18-67562983;